Starting phenix.real_space_refine on Fri Mar 15 22:32:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn8_27556/03_2024/8dn8_27556_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2340 atoms to isotropic. 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 32 5.16 5 C 7084 2.51 5 N 1666 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 6": "OD1" <-> "OD2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10638 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'U90': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'U90': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.54 Number of scatterers: 10638 At special positions: 0 Unit cell: (92.88, 98.28, 140.4, 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 32 16.00 O 1856 8.00 N 1666 7.00 C 7084 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: 3.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 14 sheets defined 45.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.549A pdb=" N ILE A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 4.681A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.910A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.921A pdb=" N GLN A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 21 through 27 removed outlier: 3.863A pdb=" N TRP B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 56 through 82 removed outlier: 3.509A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.827A pdb=" N ILE B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 89 through 92 No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 102 through 128 removed outlier: 3.790A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 4.327A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 removed outlier: 3.764A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.745A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.673A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 224 through 255 Proline residue: B 235 - end of helix removed outlier: 4.780A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 26 removed outlier: 4.004A pdb=" N PHE C 26 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 101 through 111 removed outlier: 3.811A pdb=" N ILE C 104 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TYR C 105 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 removed outlier: 4.984A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.718A pdb=" N THR C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 171 removed outlier: 4.084A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.664A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 24 through 43 removed outlier: 5.314A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.571A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 56 through 92 removed outlier: 3.644A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.990A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 128 removed outlier: 3.572A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 4.107A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 182 removed outlier: 4.484A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 194 through 202 removed outlier: 3.783A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 226 through 255 Proline residue: D 235 - end of helix removed outlier: 5.226A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.568A pdb=" N ARG A 3 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.610A pdb=" N ARG A 210 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 194 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE A 52 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 196 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY A 54 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 165 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 257 through 259 Processing sheet with id= D, first strand: chain 'A' and resid 262 through 265 Processing sheet with id= E, first strand: chain 'A' and resid 367 through 371 removed outlier: 3.743A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.621A pdb=" N VAL A 7 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 40 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS A 9 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS A 38 " --> pdb=" O LYS A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.672A pdb=" N VAL A 347 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 361 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 2 through 4 removed outlier: 3.591A pdb=" N ARG C 3 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 194 through 197 Processing sheet with id= J, first strand: chain 'C' and resid 84 through 86 removed outlier: 6.681A pdb=" N CYS C 162 " --> pdb=" O VAL C 85 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 257 through 259 removed outlier: 4.306A pdb=" N VAL C 258 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU C 287 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 262 through 265 removed outlier: 3.697A pdb=" N ARG C 263 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 283 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 367 through 371 removed outlier: 3.989A pdb=" N CYS C 367 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 345 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 349 through 351 removed outlier: 6.814A pdb=" N LYS C 351 " --> pdb=" O CYS C 359 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 359 " --> pdb=" O LYS C 351 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1158 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: 2.73 Time building geometry restraints manager: 4.38 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: 3158 1.34 - 1.46: 1903 1.46 - 1.57: 5803 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 10916 Sorted by residual: bond pdb=" N GLU C 358 " pdb=" CA GLU C 358 " ideal model delta sigma weight residual 1.462 1.498 -0.037 1.22e-02 6.72e+03 9.06e+00 bond pdb=" N PHE C 369 " pdb=" CA PHE C 369 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.67e+00 bond pdb=" N GLN C 357 " pdb=" CA GLN C 357 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.54e+00 bond pdb=" N GLU A 159 " pdb=" CA GLU A 159 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.12e+00 bond pdb=" N ASN C 368 " pdb=" CA ASN C 368 " ideal model delta sigma weight residual 1.462 1.491 -0.028 1.20e-02 6.94e+03 5.49e+00 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 96.19 - 103.75: 111 103.75 - 111.31: 4531 111.31 - 118.88: 4194 118.88 - 126.44: 5789 126.44 - 134.00: 139 Bond angle restraints: 14764 Sorted by residual: angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 112.96 108.45 4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" CA CYS C 359 " pdb=" C CYS C 359 " pdb=" O CYS C 359 " ideal model delta sigma weight residual 120.92 117.26 3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" N GLN B 12 " pdb=" CA GLN B 12 " pdb=" CB GLN B 12 " ideal model delta sigma weight residual 110.12 115.15 -5.03 1.47e+00 4.63e-01 1.17e+01 angle pdb=" N GLU C 358 " pdb=" CA GLU C 358 " pdb=" C GLU C 358 " ideal model delta sigma weight residual 107.49 113.31 -5.82 1.74e+00 3.30e-01 1.12e+01 angle pdb=" CA PHE C 369 " pdb=" CB PHE C 369 " pdb=" CG PHE C 369 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5737 17.85 - 35.71: 543 35.71 - 53.56: 90 53.56 - 71.42: 11 71.42 - 89.27: 5 Dihedral angle restraints: 6386 sinusoidal: 2606 harmonic: 3780 Sorted by residual: dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU C 88 " pdb=" C LEU C 88 " pdb=" N GLU C 89 " pdb=" CA GLU C 89 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA HIS C 187 " pdb=" C HIS C 187 " pdb=" N LYS C 188 " pdb=" CA LYS C 188 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1152 0.039 - 0.079: 365 0.079 - 0.118: 116 0.118 - 0.158: 19 0.158 - 0.197: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA PHE C 369 " pdb=" N PHE C 369 " pdb=" C PHE C 369 " pdb=" CB PHE C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA MET B 156 " pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CB MET B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1653 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 367 " 0.016 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C CYS C 367 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS C 367 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN C 368 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 152 " 0.015 2.00e-02 2.50e+03 1.57e-02 4.31e+00 pdb=" CG PHE D 152 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 152 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 152 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 152 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 152 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 358 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C GLU C 358 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU C 358 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS C 359 " -0.011 2.00e-02 2.50e+03 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 280 2.71 - 3.25: 10814 3.25 - 3.80: 16779 3.80 - 4.35: 20585 4.35 - 4.90: 35021 Nonbonded interactions: 83479 Sorted by model distance: nonbonded pdb=" OD1 ASP C 303 " pdb=" N ARG C 304 " model vdw 2.157 2.520 nonbonded pdb=" O GLU C 226 " pdb=" NE2 GLN C 230 " model vdw 2.201 2.520 nonbonded pdb=" O PHE A 134 " pdb=" OH TYR A 142 " model vdw 2.205 2.440 nonbonded pdb=" O THR A 246 " pdb=" ND2 ASN A 250 " model vdw 2.266 2.520 nonbonded pdb=" OH TYR D 60 " pdb=" O VAL D 186 " model vdw 2.266 2.440 ... (remaining 83474 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 4.030 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.130 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.003 0.041 10916 Z= 0.207 Angle : 0.610 9.381 14764 Z= 0.342 Chirality : 0.043 0.197 1656 Planarity : 0.003 0.030 1814 Dihedral : 13.761 89.269 3970 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.14 (0.24), residues: 1292 helix: 1.11 (0.22), residues: 611 sheet: -0.14 (0.43), residues: 164 loop : -1.56 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 31 HIS 0.003 0.001 HIS A 268 PHE 0.036 0.001 PHE D 152 TYR 0.018 0.001 TYR B 206 ARG 0.011 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.188 Fit side-chains REVERT: A 147 ILE cc_start: 0.9104 (mm) cc_final: 0.8782 (tp) REVERT: A 252 TYR cc_start: 0.7409 (m-80) cc_final: 0.7072 (m-80) REVERT: B 56 THR cc_start: 0.8424 (m) cc_final: 0.8031 (p) REVERT: B 167 ASP cc_start: 0.8386 (p0) cc_final: 0.7465 (p0) REVERT: C 201 MET cc_start: 0.7935 (mmp) cc_final: 0.7708 (mmm) REVERT: D 156 MET cc_start: 0.8257 (mpp) cc_final: 0.7939 (mpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2027 time to fit residues: 68.4737 Evaluate side-chains 170 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS C 230 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10916 Z= 0.170 Angle : 0.574 10.954 14764 Z= 0.295 Chirality : 0.042 0.157 1656 Planarity : 0.003 0.044 1814 Dihedral : 4.114 31.269 1412 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 10.09 % Favored : 88.19 % 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: -0.14 (0.24), residues: 1292 helix: 1.08 (0.22), residues: 606 sheet: -0.15 (0.43), residues: 164 loop : -1.48 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 8 HIS 0.006 0.001 HIS C 175 PHE 0.033 0.001 PHE C 152 TYR 0.012 0.001 TYR B 206 ARG 0.004 0.001 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.343 Fit side-chains REVERT: A 147 ILE cc_start: 0.9116 (mm) cc_final: 0.8852 (tp) REVERT: A 252 TYR cc_start: 0.7400 (m-80) cc_final: 0.7120 (m-80) REVERT: B 56 THR cc_start: 0.8579 (m) cc_final: 0.8216 (p) REVERT: B 82 THR cc_start: 0.8381 (p) cc_final: 0.8119 (p) REVERT: C 127 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: C 157 HIS cc_start: 0.8014 (m-70) cc_final: 0.7587 (t-90) REVERT: C 177 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7223 (tp-100) REVERT: C 181 PHE cc_start: 0.8956 (m-80) cc_final: 0.8221 (m-10) REVERT: C 201 MET cc_start: 0.7939 (mmp) cc_final: 0.7661 (mmm) REVERT: C 261 GLU cc_start: 0.6652 (pp20) cc_final: 0.6372 (pp20) REVERT: D 8 GLU cc_start: 0.8218 (tp30) cc_final: 0.7855 (tp30) REVERT: D 156 MET cc_start: 0.8149 (mpp) cc_final: 0.7651 (mpp) outliers start: 20 outliers final: 14 residues processed: 203 average time/residue: 0.2039 time to fit residues: 60.7382 Evaluate side-chains 183 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 147 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.0270 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10916 Z= 0.318 Angle : 0.616 11.744 14764 Z= 0.315 Chirality : 0.042 0.129 1656 Planarity : 0.003 0.031 1814 Dihedral : 4.181 24.477 1412 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.76 % Allowed : 14.66 % Favored : 82.59 % 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: -0.33 (0.24), residues: 1292 helix: 0.82 (0.22), residues: 619 sheet: -0.27 (0.42), residues: 164 loop : -1.48 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 71 HIS 0.004 0.001 HIS A 175 PHE 0.049 0.002 PHE D 152 TYR 0.017 0.001 TYR B 206 ARG 0.003 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.104 Fit side-chains REVERT: A 147 ILE cc_start: 0.9143 (mm) cc_final: 0.8938 (tp) REVERT: A 252 TYR cc_start: 0.7472 (m-80) cc_final: 0.7120 (m-80) REVERT: A 274 PHE cc_start: 0.7270 (m-10) cc_final: 0.7068 (m-10) REVERT: A 334 MET cc_start: 0.8454 (mmm) cc_final: 0.8146 (mmm) REVERT: B 167 ASP cc_start: 0.8398 (p0) cc_final: 0.7746 (p0) REVERT: C 127 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: C 157 HIS cc_start: 0.8017 (m-70) cc_final: 0.7597 (t-90) REVERT: C 177 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7836 (tp-100) REVERT: C 201 MET cc_start: 0.7971 (mmp) cc_final: 0.7646 (mmm) REVERT: C 261 GLU cc_start: 0.6857 (pp20) cc_final: 0.6577 (pp20) REVERT: D 87 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7805 (pm20) outliers start: 32 outliers final: 24 residues processed: 195 average time/residue: 0.2125 time to fit residues: 59.8779 Evaluate side-chains 185 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10916 Z= 0.289 Angle : 0.592 8.874 14764 Z= 0.303 Chirality : 0.042 0.129 1656 Planarity : 0.003 0.024 1814 Dihedral : 4.159 18.074 1412 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.45 % Allowed : 17.59 % Favored : 78.97 % 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: -0.25 (0.24), residues: 1292 helix: 0.81 (0.22), residues: 615 sheet: -0.03 (0.41), residues: 174 loop : -1.41 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 71 HIS 0.003 0.001 HIS C 175 PHE 0.022 0.002 PHE D 92 TYR 0.019 0.001 TYR B 206 ARG 0.006 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: C 127 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: C 157 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7596 (t-90) REVERT: C 177 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8026 (tp-100) REVERT: C 201 MET cc_start: 0.7996 (mmp) cc_final: 0.7645 (mmm) REVERT: C 261 GLU cc_start: 0.6961 (pp20) cc_final: 0.6695 (pp20) REVERT: C 283 GLU cc_start: 0.7343 (mp0) cc_final: 0.7082 (mp0) REVERT: C 301 ILE cc_start: 0.9325 (mt) cc_final: 0.9037 (tp) REVERT: D 156 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7268 (mpp) outliers start: 40 outliers final: 25 residues processed: 206 average time/residue: 0.2169 time to fit residues: 66.0978 Evaluate side-chains 196 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10916 Z= 0.202 Angle : 0.577 10.642 14764 Z= 0.293 Chirality : 0.041 0.162 1656 Planarity : 0.003 0.023 1814 Dihedral : 4.079 17.641 1412 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.10 % Allowed : 19.14 % Favored : 77.76 % 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: -0.20 (0.24), residues: 1292 helix: 0.94 (0.22), residues: 606 sheet: -0.08 (0.44), residues: 160 loop : -1.42 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 362 HIS 0.004 0.001 HIS C 175 PHE 0.051 0.001 PHE D 152 TYR 0.022 0.001 TYR A 252 ARG 0.005 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8279 (pt) cc_final: 0.7959 (pt) REVERT: A 274 PHE cc_start: 0.7297 (m-10) cc_final: 0.7040 (m-10) REVERT: A 334 MET cc_start: 0.8508 (mmm) cc_final: 0.8230 (mmm) REVERT: B 160 THR cc_start: 0.9343 (t) cc_final: 0.9138 (m) REVERT: C 127 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: C 157 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7535 (t-90) REVERT: C 177 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8108 (tp-100) REVERT: C 201 MET cc_start: 0.7972 (mmp) cc_final: 0.7626 (mmm) REVERT: C 230 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7822 (pp30) REVERT: C 236 MET cc_start: 0.7050 (ppp) cc_final: 0.6715 (tmm) REVERT: C 261 GLU cc_start: 0.7043 (pp20) cc_final: 0.6735 (pp20) REVERT: C 267 GLU cc_start: 0.7582 (mp0) cc_final: 0.7261 (mp0) REVERT: C 301 ILE cc_start: 0.9352 (mt) cc_final: 0.9083 (tp) REVERT: C 361 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7367 (t70) REVERT: D 156 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: D 249 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6786 (mm-30) outliers start: 36 outliers final: 26 residues processed: 201 average time/residue: 0.1951 time to fit residues: 57.3793 Evaluate side-chains 202 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 chunk 57 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10916 Z= 0.144 Angle : 0.556 10.851 14764 Z= 0.279 Chirality : 0.040 0.133 1656 Planarity : 0.003 0.024 1814 Dihedral : 3.949 16.596 1412 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.67 % Allowed : 19.14 % Favored : 78.19 % 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: -0.10 (0.24), residues: 1292 helix: 1.00 (0.22), residues: 606 sheet: -0.05 (0.44), residues: 166 loop : -1.33 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 362 HIS 0.004 0.001 HIS C 175 PHE 0.018 0.001 PHE D 175 TYR 0.015 0.001 TYR A 252 ARG 0.005 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8271 (pt) cc_final: 0.7952 (pt) REVERT: A 274 PHE cc_start: 0.7289 (m-10) cc_final: 0.7031 (m-10) REVERT: A 334 MET cc_start: 0.8433 (mmm) cc_final: 0.8196 (mmm) REVERT: C 127 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: C 157 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: C 177 GLN cc_start: 0.8349 (tp-100) cc_final: 0.8059 (tp-100) REVERT: C 201 MET cc_start: 0.7953 (mmp) cc_final: 0.7594 (mmm) REVERT: C 261 GLU cc_start: 0.6868 (pp20) cc_final: 0.6632 (pp20) REVERT: C 267 GLU cc_start: 0.7554 (mp0) cc_final: 0.7220 (mp0) REVERT: C 283 GLU cc_start: 0.7270 (mp0) cc_final: 0.6948 (mp0) REVERT: C 301 ILE cc_start: 0.9357 (mt) cc_final: 0.9117 (tp) REVERT: C 361 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7299 (t70) REVERT: D 87 GLU cc_start: 0.7906 (pm20) cc_final: 0.7456 (pm20) REVERT: D 156 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: D 249 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7016 (mm-30) outliers start: 31 outliers final: 21 residues processed: 205 average time/residue: 0.1972 time to fit residues: 59.0813 Evaluate side-chains 199 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10916 Z= 0.330 Angle : 0.629 9.486 14764 Z= 0.318 Chirality : 0.042 0.130 1656 Planarity : 0.003 0.024 1814 Dihedral : 4.169 17.714 1412 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.28 % Allowed : 20.09 % Favored : 76.64 % 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: -0.23 (0.24), residues: 1292 helix: 0.84 (0.22), residues: 608 sheet: 0.00 (0.42), residues: 174 loop : -1.39 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 71 HIS 0.003 0.001 HIS C 175 PHE 0.053 0.002 PHE D 152 TYR 0.023 0.002 TYR C 142 ARG 0.005 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8317 (pt) cc_final: 0.7985 (pt) REVERT: A 274 PHE cc_start: 0.7338 (m-10) cc_final: 0.7050 (m-10) REVERT: B 160 THR cc_start: 0.9333 (t) cc_final: 0.9096 (m) REVERT: C 127 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: C 157 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7601 (t-90) REVERT: C 177 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8203 (tp-100) REVERT: C 201 MET cc_start: 0.8043 (mmp) cc_final: 0.7698 (mmm) REVERT: C 261 GLU cc_start: 0.7115 (pp20) cc_final: 0.6885 (pp20) REVERT: C 267 GLU cc_start: 0.7574 (mp0) cc_final: 0.7242 (mp0) REVERT: C 283 GLU cc_start: 0.7169 (mp0) cc_final: 0.6840 (mp0) REVERT: C 301 ILE cc_start: 0.9371 (mt) cc_final: 0.9099 (tp) REVERT: D 87 GLU cc_start: 0.7919 (pm20) cc_final: 0.7507 (pm20) REVERT: D 156 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7453 (mtp) outliers start: 38 outliers final: 29 residues processed: 196 average time/residue: 0.2006 time to fit residues: 57.3195 Evaluate side-chains 192 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10916 Z= 0.180 Angle : 0.578 10.927 14764 Z= 0.290 Chirality : 0.040 0.132 1656 Planarity : 0.003 0.026 1814 Dihedral : 4.052 19.136 1412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.02 % Allowed : 20.69 % Favored : 76.29 % 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: -0.10 (0.25), residues: 1292 helix: 0.94 (0.22), residues: 606 sheet: 0.07 (0.42), residues: 176 loop : -1.32 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 71 HIS 0.004 0.001 HIS A 350 PHE 0.023 0.001 PHE B 175 TYR 0.022 0.001 TYR C 142 ARG 0.006 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8300 (pt) cc_final: 0.7973 (pt) REVERT: A 274 PHE cc_start: 0.7290 (m-10) cc_final: 0.7040 (m-10) REVERT: A 334 MET cc_start: 0.8508 (mmm) cc_final: 0.8156 (mmm) REVERT: C 11 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8160 (t80) REVERT: C 127 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: C 157 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: C 177 GLN cc_start: 0.8441 (tp40) cc_final: 0.8215 (tp-100) REVERT: C 201 MET cc_start: 0.8030 (mmp) cc_final: 0.7644 (mmm) REVERT: C 261 GLU cc_start: 0.7073 (pp20) cc_final: 0.6835 (pp20) REVERT: C 267 GLU cc_start: 0.7585 (mp0) cc_final: 0.7261 (mp0) REVERT: C 283 GLU cc_start: 0.7133 (mp0) cc_final: 0.6762 (mp0) REVERT: C 301 ILE cc_start: 0.9388 (mt) cc_final: 0.9119 (tp) REVERT: C 331 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7834 (p) REVERT: D 87 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: D 249 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6862 (mm-30) outliers start: 35 outliers final: 25 residues processed: 201 average time/residue: 0.2033 time to fit residues: 59.7817 Evaluate side-chains 196 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10916 Z= 0.212 Angle : 0.593 10.956 14764 Z= 0.298 Chirality : 0.041 0.175 1656 Planarity : 0.003 0.022 1814 Dihedral : 4.018 20.107 1412 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.10 % Allowed : 21.03 % Favored : 75.86 % 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: -0.12 (0.25), residues: 1292 helix: 0.95 (0.22), residues: 604 sheet: 0.01 (0.42), residues: 176 loop : -1.34 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.015 0.001 PHE D 165 TYR 0.017 0.001 TYR C 142 ARG 0.006 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8251 (pt) cc_final: 0.7931 (pt) REVERT: A 274 PHE cc_start: 0.7322 (m-10) cc_final: 0.7103 (m-10) REVERT: A 334 MET cc_start: 0.8503 (mmm) cc_final: 0.8177 (mmm) REVERT: C 11 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8158 (t80) REVERT: C 127 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: C 157 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7434 (t-90) REVERT: C 177 GLN cc_start: 0.8467 (tp40) cc_final: 0.8241 (tp-100) REVERT: C 201 MET cc_start: 0.8075 (mmp) cc_final: 0.7725 (mmm) REVERT: C 261 GLU cc_start: 0.7065 (pp20) cc_final: 0.6823 (pp20) REVERT: C 267 GLU cc_start: 0.7613 (mp0) cc_final: 0.7299 (mp0) REVERT: C 283 GLU cc_start: 0.7054 (mp0) cc_final: 0.6737 (mp0) REVERT: C 301 ILE cc_start: 0.9376 (mt) cc_final: 0.9126 (tp) REVERT: C 327 LYS cc_start: 0.9187 (tmmt) cc_final: 0.8907 (pptt) REVERT: C 331 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7806 (p) REVERT: D 87 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: D 156 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8214 (mpp) REVERT: D 249 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6909 (mm-30) outliers start: 36 outliers final: 28 residues processed: 202 average time/residue: 0.2077 time to fit residues: 61.2137 Evaluate side-chains 199 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10916 Z= 0.158 Angle : 0.586 11.565 14764 Z= 0.293 Chirality : 0.040 0.167 1656 Planarity : 0.003 0.026 1814 Dihedral : 3.924 20.629 1412 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.84 % Allowed : 22.24 % Favored : 74.91 % 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 (0.25), residues: 1292 helix: 1.02 (0.22), residues: 604 sheet: 0.03 (0.44), residues: 164 loop : -1.32 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.023 0.001 PHE D 175 TYR 0.016 0.001 TYR C 142 ARG 0.005 0.000 ARG D 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8207 (t80) REVERT: A 264 LEU cc_start: 0.8242 (pt) cc_final: 0.7911 (pt) REVERT: A 334 MET cc_start: 0.8395 (mmm) cc_final: 0.8071 (mmm) REVERT: C 127 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: C 157 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: C 177 GLN cc_start: 0.8447 (tp40) cc_final: 0.8230 (tp-100) REVERT: C 201 MET cc_start: 0.8071 (mmp) cc_final: 0.7652 (mmm) REVERT: C 261 GLU cc_start: 0.6873 (pp20) cc_final: 0.6650 (pp20) REVERT: C 267 GLU cc_start: 0.7711 (mp0) cc_final: 0.7381 (mp0) REVERT: C 283 GLU cc_start: 0.6986 (mp0) cc_final: 0.6692 (mp0) REVERT: C 301 ILE cc_start: 0.9362 (mt) cc_final: 0.9108 (tp) REVERT: C 327 LYS cc_start: 0.9193 (tmmt) cc_final: 0.8901 (pptt) REVERT: C 331 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7752 (p) REVERT: D 17 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.7921 (mmm160) REVERT: D 87 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: D 156 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8044 (mpp) REVERT: D 249 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6908 (mm-30) outliers start: 33 outliers final: 23 residues processed: 197 average time/residue: 0.2050 time to fit residues: 58.4071 Evaluate side-chains 193 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS D 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093406 restraints weight = 20326.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094734 restraints weight = 13055.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095160 restraints weight = 9527.197| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10916 Z= 0.310 Angle : 0.635 10.506 14764 Z= 0.322 Chirality : 0.042 0.149 1656 Planarity : 0.003 0.056 1814 Dihedral : 4.078 20.264 1412 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.84 % Allowed : 22.59 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1292 helix: 0.87 (0.22), residues: 604 sheet: 0.04 (0.43), residues: 175 loop : -1.34 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.016 0.002 PHE A 330 TYR 0.015 0.001 TYR B 150 ARG 0.004 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.55 seconds wall clock time: 39 minutes 34.31 seconds (2374.31 seconds total)