Starting phenix.real_space_refine on Thu Feb 15 09:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k20_22638/02_2024/7k20_22638_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7480 2.51 5 N 1984 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.24, per 1000 atoms: 0.53 Number of scatterers: 11828 At special positions: 0 Unit cell: (100.32, 77.33, 164.065, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2268 8.00 N 1984 7.00 C 7480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 16 sheets defined 34.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.636A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.676A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.765A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.751A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.732A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.751A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 359 through 365 removed outlier: 4.013A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.517A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.545A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.883A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.913A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.761A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix No H-bonds generated for 'chain 'B' and resid 253 through 258' Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 317 removed outlier: 3.667A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.837A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.629A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.512A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.514A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.737A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.658A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.685A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 293 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.516A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.074A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.848A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.503A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.666A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.538A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.897A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.653A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.699A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 338 through 346 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.105A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.852A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.401A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.859A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.927A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.317A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 134 removed outlier: 6.780A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.154A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 303 hydrogen bonds defined for protein. 780 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: 3.47 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3356 1.33 - 1.45: 2025 1.45 - 1.57: 6555 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12096 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C2 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 12091 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.91: 297 104.91 - 112.67: 6243 112.67 - 120.42: 5386 120.42 - 128.17: 4382 128.17 - 135.93: 120 Bond angle restraints: 16428 Sorted by residual: angle pdb=" C19 1T4 C 803 " pdb=" C17 1T4 C 803 " pdb=" N1 1T4 C 803 " ideal model delta sigma weight residual 114.67 125.21 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C19 1T4 B 803 " pdb=" C17 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 114.67 125.13 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 102.31 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C19 1T4 A 803 " pdb=" C17 1T4 A 803 " pdb=" N1 1T4 A 803 " ideal model delta sigma weight residual 114.67 124.77 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.28: 6950 18.28 - 36.56: 219 36.56 - 54.85: 37 54.85 - 73.13: 9 73.13 - 91.41: 5 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 -151.41 91.41 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" CA PHE C 124 " pdb=" C PHE C 124 " pdb=" N GLU C 125 " pdb=" CA GLU C 125 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N GLU A 125 " pdb=" CA GLU A 125 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1166 0.058 - 0.115: 532 0.115 - 0.172: 93 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE C 250 " pdb=" CA ILE C 250 " pdb=" CG1 ILE C 250 " pdb=" CG2 ILE C 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 250 " pdb=" CA ILE A 250 " pdb=" CG1 ILE A 250 " pdb=" CG2 ILE A 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1805 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.027 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP B 340 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 243 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO C 243 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.032 5.00e-02 4.00e+02 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 469 2.69 - 3.24: 11303 3.24 - 3.80: 18989 3.80 - 4.35: 25985 4.35 - 4.90: 43147 Nonbonded interactions: 99893 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.141 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.158 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.159 2.170 nonbonded pdb=" OE2 GLU C 270 " pdb=" OG1 THR D 203 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 802 " model vdw 2.244 2.440 ... (remaining 99888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.020 Extract box with map and model: 7.650 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.510 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.013 0.089 12096 Z= 0.829 Angle : 1.021 10.540 16428 Z= 0.521 Chirality : 0.064 0.287 1808 Planarity : 0.007 0.061 2092 Dihedral : 10.523 91.411 4468 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -5.12 (0.16), residues: 1468 helix: -4.45 (0.09), residues: 636 sheet: -2.85 (0.27), residues: 236 loop : -2.06 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 340 HIS 0.007 0.002 HIS C 40 PHE 0.030 0.004 PHE D 266 TYR 0.018 0.003 TYR C 218 ARG 0.017 0.002 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.9017 (mmm) cc_final: 0.8717 (mmm) REVERT: C 184 ASP cc_start: 0.8042 (m-30) cc_final: 0.7790 (m-30) REVERT: C 286 ASP cc_start: 0.7268 (t0) cc_final: 0.6896 (t0) REVERT: C 355 MET cc_start: 0.8304 (mmm) cc_final: 0.8081 (mmm) REVERT: D 113 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8507 (mptt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2731 time to fit residues: 52.2671 Evaluate side-chains 87 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 314 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN C 314 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12096 Z= 0.226 Angle : 0.567 7.522 16428 Z= 0.278 Chirality : 0.045 0.136 1808 Planarity : 0.005 0.050 2092 Dihedral : 8.127 85.577 1672 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.72 % Allowed : 6.13 % Favored : 93.15 % 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: -3.60 (0.19), residues: 1468 helix: -3.18 (0.15), residues: 636 sheet: -1.92 (0.30), residues: 236 loop : -1.34 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 340 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE D 200 TYR 0.008 0.001 TYR C 188 ARG 0.004 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.424 Fit side-chains REVERT: A 123 MET cc_start: 0.9079 (mmt) cc_final: 0.8800 (mmt) REVERT: A 283 MET cc_start: 0.8172 (mmm) cc_final: 0.7838 (mmm) REVERT: A 286 ASP cc_start: 0.7118 (t0) cc_final: 0.6705 (t0) REVERT: B 157 ASP cc_start: 0.7857 (t70) cc_final: 0.7592 (t0) REVERT: B 227 MET cc_start: 0.8972 (mmm) cc_final: 0.8460 (mmm) REVERT: C 355 MET cc_start: 0.8248 (mmm) cc_final: 0.7923 (mmm) REVERT: D 184 ASP cc_start: 0.7854 (m-30) cc_final: 0.7618 (m-30) REVERT: D 227 MET cc_start: 0.8920 (mmm) cc_final: 0.8712 (mmm) REVERT: D 313 MET cc_start: 0.8907 (mmm) cc_final: 0.8652 (mmm) outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.2464 time to fit residues: 40.8883 Evaluate side-chains 90 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 311 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12096 Z= 0.161 Angle : 0.517 6.059 16428 Z= 0.245 Chirality : 0.043 0.138 1808 Planarity : 0.004 0.049 2092 Dihedral : 7.313 81.942 1672 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.19 % Allowed : 6.61 % Favored : 92.20 % 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: -2.60 (0.20), residues: 1468 helix: -2.25 (0.19), residues: 612 sheet: -1.68 (0.29), residues: 236 loop : -0.89 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE C 200 TYR 0.006 0.001 TYR A 169 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.558 Fit side-chains REVERT: A 283 MET cc_start: 0.8152 (mmm) cc_final: 0.7818 (mmm) REVERT: A 349 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 157 ASP cc_start: 0.7800 (t70) cc_final: 0.7325 (t0) REVERT: C 288 ASP cc_start: 0.6711 (p0) cc_final: 0.6380 (p0) REVERT: C 355 MET cc_start: 0.8276 (mmm) cc_final: 0.7932 (mmm) REVERT: D 313 MET cc_start: 0.8868 (mmm) cc_final: 0.8664 (mmm) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 0.2390 time to fit residues: 38.7004 Evaluate side-chains 94 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 161 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12096 Z= 0.282 Angle : 0.546 7.207 16428 Z= 0.260 Chirality : 0.045 0.132 1808 Planarity : 0.004 0.046 2092 Dihedral : 7.289 80.860 1672 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.51 % Allowed : 7.48 % Favored : 91.00 % 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: -1.99 (0.21), residues: 1468 helix: -1.77 (0.20), residues: 592 sheet: -1.46 (0.30), residues: 236 loop : -0.54 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE C 124 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.392 Fit side-chains REVERT: A 187 ASP cc_start: 0.8093 (m-30) cc_final: 0.7891 (m-30) REVERT: A 283 MET cc_start: 0.8145 (mmm) cc_final: 0.7800 (mmm) REVERT: A 349 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 227 MET cc_start: 0.8858 (mmm) cc_final: 0.8475 (mmm) REVERT: C 355 MET cc_start: 0.8346 (mmm) cc_final: 0.7968 (mmm) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.2245 time to fit residues: 35.1320 Evaluate side-chains 98 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12096 Z= 0.161 Angle : 0.506 6.567 16428 Z= 0.237 Chirality : 0.043 0.133 1808 Planarity : 0.004 0.044 2092 Dihedral : 6.845 76.777 1672 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.35 % Allowed : 8.12 % Favored : 90.53 % 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: -1.67 (0.22), residues: 1468 helix: -1.57 (0.21), residues: 616 sheet: -1.17 (0.30), residues: 236 loop : -0.27 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE C 124 TYR 0.009 0.001 TYR B 294 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.420 Fit side-chains REVERT: A 283 MET cc_start: 0.8087 (mmm) cc_final: 0.7769 (mmm) REVERT: A 349 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8128 (mp) REVERT: B 227 MET cc_start: 0.8845 (mmm) cc_final: 0.8409 (mmm) REVERT: C 355 MET cc_start: 0.8298 (mmm) cc_final: 0.7901 (mmm) REVERT: D 313 MET cc_start: 0.8935 (mmm) cc_final: 0.8596 (mmm) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.2289 time to fit residues: 36.1342 Evaluate side-chains 96 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12096 Z= 0.329 Angle : 0.560 6.800 16428 Z= 0.268 Chirality : 0.046 0.128 1808 Planarity : 0.004 0.042 2092 Dihedral : 7.173 84.733 1672 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.51 % Allowed : 8.44 % Favored : 90.05 % 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: -1.53 (0.22), residues: 1468 helix: -1.52 (0.21), residues: 620 sheet: -0.94 (0.29), residues: 280 loop : -0.08 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.003 0.001 HIS C 40 PHE 0.011 0.001 PHE C 124 TYR 0.009 0.001 TYR B 294 ARG 0.003 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.463 Fit side-chains REVERT: A 283 MET cc_start: 0.8125 (mmm) cc_final: 0.7834 (mmt) REVERT: A 349 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 157 ASP cc_start: 0.7766 (t70) cc_final: 0.7377 (t0) REVERT: C 355 MET cc_start: 0.8396 (mmm) cc_final: 0.8007 (mmm) REVERT: D 313 MET cc_start: 0.8956 (mmm) cc_final: 0.8639 (mmm) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.2321 time to fit residues: 35.8238 Evaluate side-chains 100 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12096 Z= 0.173 Angle : 0.507 6.568 16428 Z= 0.238 Chirality : 0.044 0.131 1808 Planarity : 0.003 0.044 2092 Dihedral : 6.738 78.522 1672 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.75 % Allowed : 8.44 % Favored : 89.81 % 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: -1.37 (0.22), residues: 1468 helix: -1.35 (0.20), residues: 644 sheet: -0.80 (0.30), residues: 260 loop : -0.04 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE C 124 TYR 0.009 0.001 TYR D 306 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.369 Fit side-chains REVERT: A 283 MET cc_start: 0.8054 (mmm) cc_final: 0.7722 (mmm) REVERT: A 349 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 157 ASP cc_start: 0.7747 (t70) cc_final: 0.7276 (t0) REVERT: C 355 MET cc_start: 0.8356 (mmm) cc_final: 0.7969 (mmm) REVERT: D 313 MET cc_start: 0.8939 (mmm) cc_final: 0.8607 (mmm) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.2219 time to fit residues: 37.1214 Evaluate side-chains 105 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0050 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12096 Z= 0.147 Angle : 0.489 6.824 16428 Z= 0.230 Chirality : 0.043 0.131 1808 Planarity : 0.003 0.044 2092 Dihedral : 6.417 72.695 1672 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 8.60 % Favored : 89.65 % 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: -0.98 (0.23), residues: 1468 helix: -1.02 (0.22), residues: 616 sheet: -0.56 (0.30), residues: 280 loop : 0.07 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.007 0.001 PHE C 124 TYR 0.009 0.001 TYR D 133 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.246 Fit side-chains REVERT: A 283 MET cc_start: 0.8038 (mmm) cc_final: 0.7707 (mmm) REVERT: A 349 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 157 ASP cc_start: 0.7767 (t70) cc_final: 0.7290 (t0) REVERT: C 355 MET cc_start: 0.8345 (mmm) cc_final: 0.7952 (mmm) REVERT: D 101 HIS cc_start: 0.8651 (m90) cc_final: 0.8104 (m90) REVERT: D 313 MET cc_start: 0.8932 (mmm) cc_final: 0.8605 (mmm) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.2219 time to fit residues: 37.3000 Evaluate side-chains 109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12096 Z= 0.179 Angle : 0.502 7.109 16428 Z= 0.236 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.042 2092 Dihedral : 6.433 73.859 1672 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.59 % Allowed : 8.84 % Favored : 89.57 % 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: -0.80 (0.23), residues: 1468 helix: -0.86 (0.22), residues: 616 sheet: -0.42 (0.30), residues: 280 loop : 0.13 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR B 306 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.386 Fit side-chains REVERT: A 283 MET cc_start: 0.8048 (mmm) cc_final: 0.7721 (mmm) REVERT: A 349 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 157 ASP cc_start: 0.7796 (t70) cc_final: 0.7322 (t0) REVERT: C 355 MET cc_start: 0.8347 (mmm) cc_final: 0.7965 (mmm) REVERT: D 101 HIS cc_start: 0.8605 (m90) cc_final: 0.8056 (m90) REVERT: D 313 MET cc_start: 0.8934 (mmm) cc_final: 0.8607 (mmm) outliers start: 20 outliers final: 18 residues processed: 109 average time/residue: 0.2217 time to fit residues: 36.4336 Evaluate side-chains 108 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12096 Z= 0.223 Angle : 0.513 7.158 16428 Z= 0.243 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.041 2092 Dihedral : 6.580 77.441 1672 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.51 % Allowed : 9.32 % Favored : 89.17 % 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: -0.66 (0.23), residues: 1468 helix: -0.77 (0.22), residues: 608 sheet: -0.30 (0.30), residues: 288 loop : 0.20 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE C 124 TYR 0.007 0.001 TYR B 69 ARG 0.002 0.000 ARG A 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.398 Fit side-chains REVERT: A 283 MET cc_start: 0.8078 (mmm) cc_final: 0.7722 (mmm) REVERT: A 349 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 157 ASP cc_start: 0.7805 (t70) cc_final: 0.7444 (t0) REVERT: C 355 MET cc_start: 0.8339 (mmm) cc_final: 0.7974 (mmm) REVERT: D 101 HIS cc_start: 0.8640 (m90) cc_final: 0.8115 (m90) REVERT: D 288 ASP cc_start: 0.6593 (p0) cc_final: 0.6141 (p0) REVERT: D 313 MET cc_start: 0.8945 (mmm) cc_final: 0.8613 (mmm) outliers start: 19 outliers final: 18 residues processed: 108 average time/residue: 0.2229 time to fit residues: 36.3453 Evaluate side-chains 108 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.065566 restraints weight = 25299.470| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.34 r_work: 0.2809 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12096 Z= 0.184 Angle : 0.500 7.237 16428 Z= 0.236 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.043 2092 Dihedral : 6.451 74.975 1672 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.59 % Allowed : 9.24 % Favored : 89.17 % 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: -0.56 (0.23), residues: 1468 helix: -0.66 (0.22), residues: 608 sheet: -0.28 (0.32), residues: 244 loop : 0.18 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS C 161 PHE 0.007 0.001 PHE C 124 TYR 0.007 0.001 TYR B 306 ARG 0.002 0.000 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.35 seconds wall clock time: 42 minutes 15.89 seconds (2535.89 seconds total)