Starting phenix.real_space_refine on Fri Mar 15 01:35:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dne_27564/03_2024/8dne_27564_updated.pdb" } resolution = 3.5 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6841 2.51 5 N 1609 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 243": "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: 10281 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2976 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 2 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: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2979 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain breaks: 2 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.88, per 1000 atoms: 0.57 Number of scatterers: 10281 At special positions: 0 Unit cell: (91.8, 85.32, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1795 8.00 N 1609 7.00 C 6841 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: 4.35 Conformation dependent library (CDL) restraints added in 1.9 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 13 sheets defined 47.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.603A pdb=" N ILE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 115 through 129 removed outlier: 5.362A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (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 156 Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 22 through 46 removed outlier: 3.812A pdb=" N TRP B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.431A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 81 Proline residue: B 70 - end of helix 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 99 through 126 Proline residue: B 103 - end of helix removed outlier: 3.637A pdb=" N ILE B 107 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 109 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 120 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 162 removed outlier: 5.123A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Proline residue: B 141 - end of helix removed outlier: 5.259A pdb=" N ILE B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY B 155 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 162 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.851A pdb=" N LYS B 169 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE B 172 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 178 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 179 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 180 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.511A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 224 through 255 Proline residue: B 235 - end of helix removed outlier: 3.579A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 26 removed outlier: 3.561A pdb=" N LYS C 22 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 25 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.797A 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 100 through 111 Processing helix chain 'C' and resid 115 through 129 removed outlier: 4.974A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' 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: 3.694A pdb=" N THR C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.934A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 27 through 43 Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 56 through 83 Proline residue: D 70 - end of helix removed outlier: 3.613A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 99 through 128 Proline residue: D 103 - end of helix removed outlier: 5.115A pdb=" N ILE D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE D 116 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 127 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 164 removed outlier: 4.900A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Proline residue: D 141 - end of helix removed outlier: 4.789A pdb=" N TYR D 150 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER D 151 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE D 154 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY D 155 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 159 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 4.530A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (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: 3.962A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 4.362A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 234 through 255 removed outlier: 3.520A pdb=" N LEU D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 removed outlier: 5.616A pdb=" N ILE A 40 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 218 through 223 removed outlier: 6.719A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.796A pdb=" N ASP A 278 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 284 through 288 removed outlier: 3.590A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 273 through 276 removed outlier: 9.395A pdb=" N PHE A 274 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 370 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER A 276 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASN A 372 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS A 350 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 296 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.623A pdb=" N LYS A 9 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 11 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TRP A 35 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU A 33 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.506A pdb=" N VAL C 4 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 2 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.569A pdb=" N GLU C 32 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 219 through 224 removed outlier: 7.004A pdb=" N LEU C 213 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU C 222 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA C 211 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 194 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE C 52 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE C 196 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N GLY C 54 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 166 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 326 through 335 removed outlier: 3.683A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 347 through 349 Processing sheet with id= L, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.577A pdb=" N CYS C 367 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 7 through 9 removed outlier: 3.665A pdb=" N VAL C 7 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 40 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LYS C 9 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS C 38 " --> pdb=" O LYS C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 459 hydrogen bonds defined for protein. 1083 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: 2.98 Time building geometry restraints manager: 4.73 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: 3019 1.34 - 1.46: 1762 1.46 - 1.57: 5707 1.57 - 1.69: 10 1.69 - 1.81: 46 Bond restraints: 10544 Sorted by residual: bond pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.28e+00 bond pdb=" N VAL D 186 " pdb=" CA VAL D 186 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.41e-02 5.03e+03 6.38e+00 bond pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N TYR D 187 " pdb=" CA TYR D 187 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.30e+00 bond pdb=" O5' ATP C 502 " pdb=" PA ATP C 502 " ideal model delta sigma weight residual 1.579 1.602 -0.023 1.10e-02 8.26e+03 4.52e+00 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 257 106.85 - 113.65: 5818 113.65 - 120.44: 4197 120.44 - 127.24: 3893 127.24 - 134.03: 104 Bond angle restraints: 14269 Sorted by residual: angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 127.51 9.32 1.00e+00 1.00e+00 8.69e+01 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 131.01 8.86 1.00e+00 1.00e+00 7.85e+01 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.39e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" C5' ATP A 502 " pdb=" O5' ATP A 502 " pdb=" PA ATP A 502 " ideal model delta sigma weight residual 121.27 116.98 4.29 1.00e+00 1.00e+00 1.84e+01 ... (remaining 14264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5533 17.98 - 35.95: 544 35.95 - 53.93: 107 53.93 - 71.90: 12 71.90 - 89.88: 11 Dihedral angle restraints: 6207 sinusoidal: 2568 harmonic: 3639 Sorted by residual: dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N LYS A 28 " pdb=" CA LYS A 28 " ideal model delta harmonic sigma weight residual 180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN C 95 " pdb=" C ASN C 95 " pdb=" N TYR C 96 " pdb=" CA TYR C 96 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP C 200 " pdb=" C ASP C 200 " pdb=" N MET C 201 " pdb=" CA MET C 201 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1461 0.074 - 0.147: 139 0.147 - 0.221: 3 0.221 - 0.294: 0 0.294 - 0.368: 2 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA VAL D 186 " pdb=" N VAL D 186 " pdb=" C VAL D 186 " pdb=" CB VAL D 186 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL B 186 " pdb=" N VAL B 186 " pdb=" C VAL B 186 " pdb=" CB VAL B 186 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1602 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 31 " -0.020 2.00e-02 2.50e+03 1.97e-02 9.71e+00 pdb=" CG TRP D 31 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 31 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 31 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 31 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 193 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO D 194 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 31 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 32 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.035 5.00e-02 4.00e+02 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 28 2.41 - 3.03: 6160 3.03 - 3.65: 15122 3.65 - 4.28: 21893 4.28 - 4.90: 37099 Nonbonded interactions: 80302 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O1G ATP C 502 " model vdw 1.785 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 1.995 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B ATP A 502 " model vdw 2.020 2.170 nonbonded pdb=" O SER D 119 " pdb=" OG1 THR D 122 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR D 206 " pdb=" O ASP D 221 " model vdw 2.219 2.440 ... (remaining 80297 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' and (resid 1 through 240 or resid 254 through 350 or resid 363 throug \ h 393 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 350 or resid 363 through 393 or resid 501 throug \ h 502)) } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.560 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10544 Z= 0.229 Angle : 0.654 9.547 14269 Z= 0.382 Chirality : 0.044 0.368 1605 Planarity : 0.004 0.063 1737 Dihedral : 14.834 89.879 3875 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.37 (0.24), residues: 1235 helix: 0.40 (0.22), residues: 574 sheet: 0.67 (0.37), residues: 198 loop : -1.42 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 31 HIS 0.004 0.001 HIS D 45 PHE 0.018 0.001 PHE C 30 TYR 0.021 0.001 TYR B 150 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.134 Fit side-chains REVERT: B 187 TYR cc_start: 0.8141 (p90) cc_final: 0.7819 (p90) REVERT: C 317 MET cc_start: 0.7857 (mtp) cc_final: 0.7651 (mtp) REVERT: C 362 TRP cc_start: 0.7203 (t60) cc_final: 0.6447 (m-90) REVERT: D 87 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6585 (tm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1986 time to fit residues: 51.2701 Evaluate side-chains 138 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 53 HIS C 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10544 Z= 0.196 Angle : 0.550 7.959 14269 Z= 0.289 Chirality : 0.042 0.165 1605 Planarity : 0.004 0.050 1737 Dihedral : 8.370 89.559 1411 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.80 % Allowed : 10.71 % Favored : 88.48 % 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: -0.22 (0.24), residues: 1235 helix: 0.53 (0.22), residues: 581 sheet: 0.72 (0.37), residues: 199 loop : -1.37 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 31 HIS 0.006 0.001 HIS B 53 PHE 0.026 0.001 PHE D 72 TYR 0.019 0.001 TYR B 150 ARG 0.004 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5413 (ptt-90) cc_final: 0.4982 (ptp90) REVERT: B 187 TYR cc_start: 0.8500 (p90) cc_final: 0.8088 (p90) REVERT: C 236 MET cc_start: 0.7730 (mmt) cc_final: 0.7517 (mmm) REVERT: C 362 TRP cc_start: 0.7117 (t60) cc_final: 0.6420 (m-90) REVERT: D 8 GLU cc_start: 0.7452 (tp30) cc_final: 0.6501 (tp30) outliers start: 9 outliers final: 7 residues processed: 159 average time/residue: 0.1869 time to fit residues: 44.1747 Evaluate side-chains 150 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 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 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10544 Z= 0.323 Angle : 0.605 7.824 14269 Z= 0.316 Chirality : 0.044 0.171 1605 Planarity : 0.004 0.049 1737 Dihedral : 8.724 89.620 1411 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.61 % Allowed : 14.73 % Favored : 83.66 % 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: -0.46 (0.24), residues: 1235 helix: 0.34 (0.22), residues: 591 sheet: 0.69 (0.37), residues: 195 loop : -1.58 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 31 HIS 0.004 0.001 HIS D 45 PHE 0.026 0.002 PHE D 72 TYR 0.025 0.001 TYR B 150 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5315 (ptt-90) cc_final: 0.4968 (ptp90) REVERT: A 315 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.4735 (t80) REVERT: B 54 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: B 187 TYR cc_start: 0.8714 (p90) cc_final: 0.8229 (p90) REVERT: C 362 TRP cc_start: 0.7268 (t60) cc_final: 0.6443 (m-90) REVERT: D 179 PHE cc_start: 0.8638 (t80) cc_final: 0.8416 (t80) outliers start: 18 outliers final: 11 residues processed: 162 average time/residue: 0.1880 time to fit residues: 45.4414 Evaluate side-chains 148 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10544 Z= 0.152 Angle : 0.516 8.265 14269 Z= 0.271 Chirality : 0.041 0.171 1605 Planarity : 0.004 0.041 1737 Dihedral : 8.106 89.857 1411 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.96 % Allowed : 16.34 % Favored : 81.70 % 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: -0.26 (0.24), residues: 1235 helix: 0.52 (0.22), residues: 581 sheet: 0.79 (0.37), residues: 193 loop : -1.45 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 31 HIS 0.005 0.001 HIS D 45 PHE 0.028 0.001 PHE D 72 TYR 0.014 0.001 TYR B 243 ARG 0.006 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5130 (ptt-90) cc_final: 0.4783 (ptp90) REVERT: B 89 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8344 (ttpp) REVERT: B 187 TYR cc_start: 0.8520 (p90) cc_final: 0.7996 (p90) REVERT: C 362 TRP cc_start: 0.7187 (t60) cc_final: 0.6427 (m-90) REVERT: D 33 ILE cc_start: 0.8222 (mp) cc_final: 0.7937 (mp) REVERT: D 172 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7852 (tp) REVERT: D 175 PHE cc_start: 0.8381 (t80) cc_final: 0.8142 (t80) REVERT: D 179 PHE cc_start: 0.8586 (t80) cc_final: 0.8338 (t80) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.1867 time to fit residues: 44.4472 Evaluate side-chains 154 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS C 103 ASN D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10544 Z= 0.476 Angle : 0.698 7.765 14269 Z= 0.364 Chirality : 0.047 0.183 1605 Planarity : 0.005 0.046 1737 Dihedral : 8.555 88.675 1411 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.48 % Allowed : 17.23 % Favored : 79.29 % 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: -0.77 (0.24), residues: 1235 helix: 0.02 (0.21), residues: 604 sheet: 0.40 (0.37), residues: 201 loop : -1.63 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 31 HIS 0.013 0.002 HIS B 53 PHE 0.026 0.002 PHE D 72 TYR 0.030 0.002 TYR B 150 ARG 0.004 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 263 ARG cc_start: 0.5537 (ptt-90) cc_final: 0.5033 (ptp90) REVERT: A 375 LYS cc_start: 0.8430 (tmmt) cc_final: 0.8085 (ttpp) REVERT: B 54 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: B 80 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7947 (ttp-170) REVERT: B 187 TYR cc_start: 0.8736 (p90) cc_final: 0.7943 (p90) REVERT: D 8 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 11 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7918 (ttm-80) REVERT: D 12 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: D 33 ILE cc_start: 0.8344 (mt) cc_final: 0.8044 (mp) REVERT: D 37 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7551 (mm) REVERT: D 47 ILE cc_start: 0.5736 (OUTLIER) cc_final: 0.5384 (mp) REVERT: D 179 PHE cc_start: 0.8689 (t80) cc_final: 0.8423 (t80) outliers start: 39 outliers final: 23 residues processed: 169 average time/residue: 0.1865 time to fit residues: 46.2806 Evaluate side-chains 165 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10544 Z= 0.191 Angle : 0.543 8.175 14269 Z= 0.288 Chirality : 0.042 0.188 1605 Planarity : 0.004 0.042 1737 Dihedral : 7.883 84.243 1411 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.04 % Allowed : 19.11 % Favored : 77.86 % 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: -0.38 (0.24), residues: 1235 helix: 0.35 (0.22), residues: 596 sheet: 0.65 (0.36), residues: 203 loop : -1.47 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 31 HIS 0.012 0.001 HIS B 53 PHE 0.031 0.001 PHE D 72 TYR 0.018 0.001 TYR C 391 ARG 0.006 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5405 (ptt-90) cc_final: 0.5020 (ptp90) REVERT: A 375 LYS cc_start: 0.8471 (tmmt) cc_final: 0.8116 (ttpp) REVERT: B 89 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8391 (ttpp) REVERT: C 362 TRP cc_start: 0.7146 (t60) cc_final: 0.6246 (m-90) REVERT: D 11 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7872 (ttm-80) REVERT: D 33 ILE cc_start: 0.8327 (mt) cc_final: 0.8062 (mp) REVERT: D 179 PHE cc_start: 0.8584 (t80) cc_final: 0.8350 (t80) outliers start: 34 outliers final: 23 residues processed: 160 average time/residue: 0.2020 time to fit residues: 47.9651 Evaluate side-chains 155 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 26 TRP Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10544 Z= 0.242 Angle : 0.563 8.133 14269 Z= 0.296 Chirality : 0.042 0.193 1605 Planarity : 0.004 0.043 1737 Dihedral : 7.709 82.423 1411 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.50 % Allowed : 20.27 % Favored : 77.23 % 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: -0.38 (0.24), residues: 1235 helix: 0.39 (0.22), residues: 595 sheet: 0.72 (0.37), residues: 201 loop : -1.55 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 31 HIS 0.008 0.001 HIS B 53 PHE 0.030 0.001 PHE D 175 TYR 0.020 0.001 TYR B 150 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5467 (ptt-90) cc_final: 0.5030 (ptp90) REVERT: A 375 LYS cc_start: 0.8452 (tmmt) cc_final: 0.8184 (ttpp) REVERT: B 89 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8394 (ttpp) REVERT: C 362 TRP cc_start: 0.7231 (t60) cc_final: 0.6949 (t60) REVERT: D 8 GLU cc_start: 0.7521 (tp30) cc_final: 0.6884 (tp30) REVERT: D 12 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: D 179 PHE cc_start: 0.8613 (t80) cc_final: 0.8391 (t80) outliers start: 28 outliers final: 23 residues processed: 156 average time/residue: 0.1931 time to fit residues: 44.2673 Evaluate side-chains 157 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10544 Z= 0.181 Angle : 0.537 8.205 14269 Z= 0.282 Chirality : 0.041 0.197 1605 Planarity : 0.004 0.043 1737 Dihedral : 7.364 80.924 1411 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.77 % Allowed : 20.45 % Favored : 76.79 % 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: -0.28 (0.24), residues: 1235 helix: 0.47 (0.22), residues: 596 sheet: 0.79 (0.37), residues: 199 loop : -1.51 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 31 HIS 0.005 0.001 HIS D 45 PHE 0.032 0.001 PHE D 175 TYR 0.018 0.001 TYR C 391 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5529 (ptt-90) cc_final: 0.5129 (ptp90) REVERT: A 375 LYS cc_start: 0.8445 (tmmt) cc_final: 0.8092 (ttpp) REVERT: B 89 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8392 (ttpp) REVERT: C 362 TRP cc_start: 0.7277 (t60) cc_final: 0.6952 (t60) REVERT: D 8 GLU cc_start: 0.7507 (tp30) cc_final: 0.6738 (tp30) REVERT: D 12 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7464 (mt0) outliers start: 31 outliers final: 26 residues processed: 162 average time/residue: 0.1953 time to fit residues: 46.5975 Evaluate side-chains 167 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10544 Z= 0.219 Angle : 0.559 8.113 14269 Z= 0.295 Chirality : 0.042 0.215 1605 Planarity : 0.004 0.045 1737 Dihedral : 7.294 80.456 1411 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.59 % Allowed : 20.89 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1235 helix: 0.47 (0.22), residues: 596 sheet: 0.76 (0.36), residues: 208 loop : -1.49 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 31 HIS 0.006 0.001 HIS B 53 PHE 0.035 0.001 PHE D 175 TYR 0.019 0.001 TYR B 150 ARG 0.005 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5520 (ptt-90) cc_final: 0.5099 (ptp90) REVERT: A 375 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8090 (ttpp) REVERT: B 80 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7147 (ttp-170) REVERT: B 89 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8400 (ttpp) REVERT: C 362 TRP cc_start: 0.7282 (t60) cc_final: 0.6931 (t60) REVERT: D 8 GLU cc_start: 0.7571 (tp30) cc_final: 0.6787 (tp30) REVERT: D 12 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7536 (mt0) outliers start: 29 outliers final: 26 residues processed: 157 average time/residue: 0.1992 time to fit residues: 46.0462 Evaluate side-chains 161 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10544 Z= 0.200 Angle : 0.554 8.181 14269 Z= 0.293 Chirality : 0.043 0.439 1605 Planarity : 0.004 0.044 1737 Dihedral : 7.162 80.215 1411 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.59 % Allowed : 21.25 % Favored : 76.16 % 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: 1235 helix: 0.47 (0.22), residues: 602 sheet: 0.78 (0.36), residues: 208 loop : -1.47 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 31 HIS 0.007 0.001 HIS B 53 PHE 0.035 0.001 PHE D 175 TYR 0.018 0.001 TYR C 391 ARG 0.006 0.000 ARG D 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5520 (ptt-90) cc_final: 0.5107 (ptp90) REVERT: A 375 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8068 (ttpp) REVERT: B 89 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8391 (ttpp) REVERT: C 362 TRP cc_start: 0.7370 (t60) cc_final: 0.7031 (t60) REVERT: D 8 GLU cc_start: 0.7495 (tp30) cc_final: 0.6706 (tp30) REVERT: D 12 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7523 (mt0) outliers start: 29 outliers final: 26 residues processed: 157 average time/residue: 0.1998 time to fit residues: 46.0864 Evaluate side-chains 160 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0010 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129197 restraints weight = 15690.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134948 restraints weight = 8919.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136697 restraints weight = 5677.933| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10544 Z= 0.146 Angle : 0.546 13.247 14269 Z= 0.283 Chirality : 0.043 0.448 1605 Planarity : 0.004 0.044 1737 Dihedral : 6.881 81.060 1411 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.41 % Allowed : 21.43 % Favored : 76.16 % 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: 1235 helix: 0.48 (0.22), residues: 595 sheet: 0.82 (0.36), residues: 206 loop : -1.41 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 31 HIS 0.006 0.001 HIS B 53 PHE 0.034 0.001 PHE D 175 TYR 0.018 0.001 TYR C 391 ARG 0.006 0.000 ARG D 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.27 seconds wall clock time: 35 minutes 20.17 seconds (2120.17 seconds total)