Starting phenix.real_space_refine on Wed Feb 14 23:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9x_22755/02_2024/7k9x_22755.pdb" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 6.07, per 1000 atoms: 0.58 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 79.17, 106.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.730A pdb=" N LYS A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.636A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.538A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 31 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 564 hydrogen bonds defined for protein. 1608 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: 2.91 Time building geometry restraints manager: 4.58 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: 3443 1.34 - 1.46: 1851 1.46 - 1.57: 5322 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.87e+00 bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.77e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" CB GLU B 14 " pdb=" CG GLU B 14 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 348 106.59 - 113.43: 6013 113.43 - 120.27: 3900 120.27 - 127.11: 4078 127.11 - 133.95: 125 Bond angle restraints: 14464 Sorted by residual: angle pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 121.19 129.32 -8.13 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta sigma weight residual 121.19 129.31 -8.12 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 121.19 129.27 -8.08 1.59e+00 3.96e-01 2.58e+01 angle pdb=" C ASN C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 121.19 129.26 -8.07 1.59e+00 3.96e-01 2.58e+01 angle pdb=" CA GLU C 49 " pdb=" CB GLU C 49 " pdb=" CG GLU C 49 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.47e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 5733 16.52 - 33.03: 591 33.03 - 49.55: 112 49.55 - 66.07: 56 66.07 - 82.58: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA VAL C 264 " pdb=" C VAL C 264 " pdb=" N THR C 265 " pdb=" CA THR C 265 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL A 264 " pdb=" C VAL A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL B 264 " pdb=" C VAL B 264 " pdb=" N THR B 265 " pdb=" CA THR B 265 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1094 0.044 - 0.088: 390 0.088 - 0.133: 116 0.133 - 0.177: 32 0.177 - 0.221: 12 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE B 46 " pdb=" CA ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CG2 ILE B 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 46 " pdb=" CA ILE C 46 " pdb=" CG1 ILE C 46 " pdb=" CG2 ILE C 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 46 " pdb=" CA ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CG2 ILE A 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 329 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS D 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS D 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 330 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS C 329 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C LYS A 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2592 2.78 - 3.31: 9896 3.31 - 3.84: 18124 3.84 - 4.37: 21109 4.37 - 4.90: 35941 Nonbonded interactions: 87662 Sorted by model distance: nonbonded pdb=" O MET D 250 " pdb=" OG1 THR D 254 " model vdw 2.254 2.440 nonbonded pdb=" O MET A 250 " pdb=" OG1 THR A 254 " model vdw 2.254 2.440 nonbonded pdb=" O MET B 250 " pdb=" OG1 THR B 254 " model vdw 2.254 2.440 nonbonded pdb=" O MET C 250 " pdb=" OG1 THR C 254 " model vdw 2.254 2.440 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.259 2.440 ... (remaining 87657 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 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: 5.200 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: 0.000 Extract box with map and model: 5.680 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.870 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.008 0.054 10672 Z= 0.525 Angle : 0.961 8.127 14464 Z= 0.549 Chirality : 0.053 0.221 1644 Planarity : 0.008 0.049 1880 Dihedral : 15.204 82.581 3984 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.12 % Allowed : 6.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.20), residues: 1364 helix: -1.10 (0.16), residues: 672 sheet: -2.01 (0.33), residues: 200 loop : -0.99 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 295 HIS 0.005 0.001 HIS C 156 PHE 0.017 0.003 PHE A 144 TYR 0.017 0.003 TYR A 213 ARG 0.007 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 323 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 57 PHE cc_start: 0.8580 (t80) cc_final: 0.7816 (t80) REVERT: B 60 GLN cc_start: 0.8499 (mt0) cc_final: 0.8107 (mt0) REVERT: B 79 PHE cc_start: 0.9009 (t80) cc_final: 0.8610 (t80) REVERT: B 100 LYS cc_start: 0.8013 (pttt) cc_final: 0.7758 (ptmt) REVERT: B 127 LEU cc_start: 0.8329 (mt) cc_final: 0.7370 (pt) REVERT: B 250 MET cc_start: 0.8119 (tpp) cc_final: 0.7879 (tpt) REVERT: B 278 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 310 LEU cc_start: 0.9174 (tp) cc_final: 0.8824 (tt) REVERT: B 311 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9133 (tptt) REVERT: A 49 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: A 57 PHE cc_start: 0.8357 (t80) cc_final: 0.7534 (t80) REVERT: A 58 TYR cc_start: 0.8431 (t80) cc_final: 0.8086 (t80) REVERT: A 91 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7793 (ptp-110) REVERT: A 185 ILE cc_start: 0.9085 (mt) cc_final: 0.8854 (tt) REVERT: A 233 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7877 (p) REVERT: A 250 MET cc_start: 0.8164 (tpp) cc_final: 0.7879 (tpt) REVERT: A 278 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 310 LEU cc_start: 0.9127 (tp) cc_final: 0.8813 (tt) REVERT: A 321 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7775 (tptp) REVERT: C 61 LEU cc_start: 0.8793 (tt) cc_final: 0.8472 (tt) REVERT: C 86 LYS cc_start: 0.7455 (mttt) cc_final: 0.7255 (ttmm) REVERT: C 93 PHE cc_start: 0.8954 (m-10) cc_final: 0.8732 (m-80) REVERT: C 185 ILE cc_start: 0.9070 (mt) cc_final: 0.8747 (tt) REVERT: C 250 MET cc_start: 0.8270 (tpp) cc_final: 0.7907 (tpt) REVERT: C 278 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 310 LEU cc_start: 0.9174 (tp) cc_final: 0.8899 (tt) REVERT: C 324 GLN cc_start: 0.7521 (mt0) cc_final: 0.6663 (tm-30) REVERT: D 38 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8549 (p) REVERT: D 57 PHE cc_start: 0.8556 (t80) cc_final: 0.8264 (t80) REVERT: D 100 LYS cc_start: 0.7794 (pttt) cc_final: 0.7530 (ptmt) REVERT: D 195 ASP cc_start: 0.8420 (p0) cc_final: 0.8064 (p0) REVERT: D 278 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8310 (mt-10) outliers start: 68 outliers final: 10 residues processed: 364 average time/residue: 0.3058 time to fit residues: 146.4537 Evaluate side-chains 225 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS B 287 ASN A 125 GLN A 168 ASN A 220 HIS C 80 HIS C 125 GLN C 339 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN D 237 HIS D 282 ASN D 287 ASN D 339 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.187 Angle : 0.600 8.364 14464 Z= 0.308 Chirality : 0.040 0.128 1644 Planarity : 0.005 0.041 1880 Dihedral : 6.548 101.568 1494 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.16 % Allowed : 14.12 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.08 (0.22), residues: 1364 helix: 1.02 (0.19), residues: 684 sheet: -1.22 (0.36), residues: 184 loop : -0.67 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 147 HIS 0.005 0.001 HIS D 237 PHE 0.028 0.001 PHE D 79 TYR 0.024 0.002 TYR A 203 ARG 0.006 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7494 (ptm160) REVERT: B 57 PHE cc_start: 0.8315 (t80) cc_final: 0.8089 (t80) REVERT: B 79 PHE cc_start: 0.8963 (t80) cc_final: 0.8674 (t80) REVERT: B 127 LEU cc_start: 0.8200 (mt) cc_final: 0.7343 (pp) REVERT: B 185 ILE cc_start: 0.8945 (mt) cc_final: 0.8634 (tt) REVERT: B 206 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 250 MET cc_start: 0.8199 (tpp) cc_final: 0.7846 (mmt) REVERT: B 339 GLN cc_start: 0.7293 (pt0) cc_final: 0.6986 (pt0) REVERT: A 119 ASN cc_start: 0.8628 (t0) cc_final: 0.8418 (t0) REVERT: A 242 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8284 (tttm) REVERT: C 42 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7455 (mmm-85) REVERT: C 185 ILE cc_start: 0.9081 (mt) cc_final: 0.8832 (tt) REVERT: C 233 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7597 (p) REVERT: C 242 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8319 (tttm) REVERT: C 250 MET cc_start: 0.8385 (tpp) cc_final: 0.8013 (tpt) REVERT: C 283 LEU cc_start: 0.8669 (tp) cc_final: 0.8308 (mt) REVERT: C 301 TYR cc_start: 0.7772 (m-10) cc_final: 0.7097 (m-80) REVERT: D 57 PHE cc_start: 0.8345 (t80) cc_final: 0.7829 (t80) REVERT: D 60 GLN cc_start: 0.8410 (mt0) cc_final: 0.8147 (mt0) REVERT: D 79 PHE cc_start: 0.8665 (t80) cc_final: 0.8404 (t80) REVERT: D 100 LYS cc_start: 0.7556 (ptmt) cc_final: 0.7164 (ttpt) REVERT: D 195 ASP cc_start: 0.8329 (p0) cc_final: 0.7996 (p0) REVERT: D 206 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8222 (mm-30) REVERT: D 339 GLN cc_start: 0.7846 (pt0) cc_final: 0.7551 (pt0) outliers start: 24 outliers final: 13 residues processed: 263 average time/residue: 0.2723 time to fit residues: 97.0218 Evaluate side-chains 218 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 chunk 99 optimal weight: 3.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS B 339 GLN A 168 ASN A 339 GLN C 80 HIS C 282 ASN C 339 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10672 Z= 0.160 Angle : 0.573 8.445 14464 Z= 0.291 Chirality : 0.040 0.123 1644 Planarity : 0.004 0.029 1880 Dihedral : 4.383 20.051 1472 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.52 % Allowed : 16.37 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.87 (0.23), residues: 1364 helix: 1.70 (0.19), residues: 688 sheet: -0.81 (0.36), residues: 184 loop : -0.38 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 313 HIS 0.010 0.001 HIS C 80 PHE 0.020 0.002 PHE D 79 TYR 0.022 0.002 TYR B 203 ARG 0.005 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 245 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8161 (ptm-80) cc_final: 0.7709 (ptm160) REVERT: B 79 PHE cc_start: 0.8954 (t80) cc_final: 0.8667 (t80) REVERT: B 127 LEU cc_start: 0.8267 (mt) cc_final: 0.7376 (pp) REVERT: B 185 ILE cc_start: 0.8887 (mt) cc_final: 0.8581 (tt) REVERT: B 250 MET cc_start: 0.8194 (tpp) cc_final: 0.7911 (tpt) REVERT: B 271 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7789 (m) REVERT: A 119 ASN cc_start: 0.8646 (t0) cc_final: 0.8415 (t0) REVERT: A 222 TYR cc_start: 0.8809 (t80) cc_final: 0.8390 (t80) REVERT: A 292 LEU cc_start: 0.7530 (mm) cc_final: 0.7270 (mp) REVERT: A 303 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7745 (mtp180) REVERT: C 42 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7464 (mmm-85) REVERT: C 57 PHE cc_start: 0.8277 (t80) cc_final: 0.7702 (t80) REVERT: C 185 ILE cc_start: 0.9079 (mt) cc_final: 0.8831 (tt) REVERT: C 222 TYR cc_start: 0.8753 (t80) cc_final: 0.8271 (t80) REVERT: C 250 MET cc_start: 0.8304 (tpp) cc_final: 0.7971 (tpt) REVERT: C 301 TYR cc_start: 0.7754 (m-10) cc_final: 0.7531 (m-80) REVERT: D 57 PHE cc_start: 0.8308 (t80) cc_final: 0.7817 (t80) REVERT: D 60 GLN cc_start: 0.8381 (mt0) cc_final: 0.8151 (mt0) REVERT: D 79 PHE cc_start: 0.8718 (t80) cc_final: 0.8442 (t80) REVERT: D 100 LYS cc_start: 0.7550 (ptmt) cc_final: 0.7203 (ttpt) REVERT: D 195 ASP cc_start: 0.8297 (p0) cc_final: 0.7967 (p0) outliers start: 28 outliers final: 19 residues processed: 260 average time/residue: 0.2401 time to fit residues: 87.2478 Evaluate side-chains 225 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 190 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN A 168 ASN A 339 GLN C 282 ASN D 80 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10672 Z= 0.176 Angle : 0.561 8.338 14464 Z= 0.286 Chirality : 0.040 0.223 1644 Planarity : 0.004 0.028 1880 Dihedral : 4.267 18.883 1472 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.78 % Allowed : 17.00 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.08 (0.23), residues: 1364 helix: 1.96 (0.19), residues: 688 sheet: -0.99 (0.34), residues: 200 loop : -0.26 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 313 HIS 0.010 0.001 HIS C 80 PHE 0.016 0.002 PHE D 79 TYR 0.021 0.002 TYR B 203 ARG 0.006 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8039 (ptm-80) cc_final: 0.7622 (ptm160) REVERT: B 79 PHE cc_start: 0.8934 (t80) cc_final: 0.8572 (t80) REVERT: B 127 LEU cc_start: 0.8401 (mt) cc_final: 0.7571 (pt) REVERT: B 185 ILE cc_start: 0.8995 (mt) cc_final: 0.8727 (tt) REVERT: B 250 MET cc_start: 0.8233 (tpp) cc_final: 0.7848 (mmt) REVERT: B 269 PHE cc_start: 0.8556 (m-80) cc_final: 0.7777 (m-80) REVERT: B 271 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7710 (m) REVERT: A 119 ASN cc_start: 0.8637 (t0) cc_final: 0.8412 (t0) REVERT: A 127 LEU cc_start: 0.8939 (mt) cc_final: 0.8259 (pt) REVERT: C 42 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7561 (mmm-85) REVERT: C 185 ILE cc_start: 0.9068 (mt) cc_final: 0.8771 (tt) REVERT: C 242 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8377 (tttm) REVERT: C 250 MET cc_start: 0.8264 (tpp) cc_final: 0.7969 (tpt) REVERT: C 283 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8698 (mt) REVERT: C 301 TYR cc_start: 0.7599 (m-10) cc_final: 0.7218 (m-10) REVERT: D 57 PHE cc_start: 0.8292 (t80) cc_final: 0.7799 (t80) REVERT: D 60 GLN cc_start: 0.8310 (mt0) cc_final: 0.8078 (mt0) REVERT: D 100 LYS cc_start: 0.7590 (ptmt) cc_final: 0.7211 (ttpt) REVERT: D 195 ASP cc_start: 0.8323 (p0) cc_final: 0.7992 (p0) REVERT: D 206 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 271 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7483 (m) REVERT: D 278 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: D 310 LEU cc_start: 0.9047 (mt) cc_final: 0.8775 (mt) outliers start: 42 outliers final: 31 residues processed: 249 average time/residue: 0.2422 time to fit residues: 85.3070 Evaluate side-chains 231 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 339 GLN C 282 ASN C 339 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.195 Angle : 0.570 7.851 14464 Z= 0.291 Chirality : 0.040 0.182 1644 Planarity : 0.004 0.029 1880 Dihedral : 4.229 19.697 1472 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.69 % Allowed : 18.35 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.24 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 688 sheet: -0.93 (0.34), residues: 200 loop : -0.18 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 147 HIS 0.009 0.001 HIS D 80 PHE 0.038 0.002 PHE A 79 TYR 0.030 0.002 TYR A 301 ARG 0.006 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7683 (ptm160) REVERT: B 79 PHE cc_start: 0.8909 (t80) cc_final: 0.8636 (t80) REVERT: B 127 LEU cc_start: 0.8531 (mt) cc_final: 0.7691 (pt) REVERT: B 185 ILE cc_start: 0.9077 (mt) cc_final: 0.8849 (tt) REVERT: B 250 MET cc_start: 0.8260 (tpp) cc_final: 0.7880 (mmt) REVERT: B 271 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7625 (m) REVERT: B 326 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: A 119 ASN cc_start: 0.8675 (t0) cc_final: 0.8375 (t0) REVERT: A 189 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7079 (tt0) REVERT: A 206 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 222 TYR cc_start: 0.8828 (t80) cc_final: 0.8572 (t80) REVERT: A 242 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8391 (tttm) REVERT: C 42 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7563 (mmm-85) REVERT: C 173 TYR cc_start: 0.8446 (t80) cc_final: 0.8239 (t80) REVERT: C 185 ILE cc_start: 0.9012 (mt) cc_final: 0.8758 (tt) REVERT: C 189 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7127 (tt0) REVERT: C 242 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8487 (tttm) REVERT: C 325 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7970 (pp20) REVERT: D 57 PHE cc_start: 0.8300 (t80) cc_final: 0.7809 (t80) REVERT: D 60 GLN cc_start: 0.8302 (mt0) cc_final: 0.8060 (mt0) REVERT: D 100 LYS cc_start: 0.7642 (ptmt) cc_final: 0.7237 (ttpt) REVERT: D 195 ASP cc_start: 0.8345 (p0) cc_final: 0.8026 (p0) REVERT: D 271 SER cc_start: 0.7868 (OUTLIER) cc_final: 0.7430 (m) REVERT: D 310 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8772 (mt) outliers start: 41 outliers final: 28 residues processed: 242 average time/residue: 0.2338 time to fit residues: 78.5380 Evaluate side-chains 225 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN C 282 ASN D 54 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN D 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.169 Angle : 0.558 8.435 14464 Z= 0.285 Chirality : 0.040 0.171 1644 Planarity : 0.004 0.029 1880 Dihedral : 4.136 17.547 1472 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.69 % Allowed : 18.44 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.35 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 688 sheet: -0.84 (0.34), residues: 200 loop : -0.14 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.004 0.000 HIS B 237 PHE 0.025 0.001 PHE D 79 TYR 0.036 0.002 TYR C 222 ARG 0.007 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7631 (ptm160) REVERT: B 79 PHE cc_start: 0.8865 (t80) cc_final: 0.8599 (t80) REVERT: B 127 LEU cc_start: 0.8548 (mt) cc_final: 0.7749 (pt) REVERT: B 250 MET cc_start: 0.8263 (tpp) cc_final: 0.7955 (mmt) REVERT: B 271 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7386 (m) REVERT: B 326 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: A 206 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 222 TYR cc_start: 0.8859 (t80) cc_final: 0.8546 (t80) REVERT: A 242 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8451 (tttm) REVERT: C 42 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7564 (mmm-85) REVERT: C 189 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7210 (tt0) REVERT: C 195 ASP cc_start: 0.7368 (t0) cc_final: 0.7049 (m-30) REVERT: C 242 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8454 (tttm) REVERT: C 283 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8712 (mt) REVERT: C 301 TYR cc_start: 0.7516 (m-10) cc_final: 0.7110 (m-80) REVERT: C 325 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7989 (pp20) REVERT: D 57 PHE cc_start: 0.8222 (t80) cc_final: 0.7771 (t80) REVERT: D 58 TYR cc_start: 0.8489 (t80) cc_final: 0.8051 (t80) REVERT: D 100 LYS cc_start: 0.7691 (ptmt) cc_final: 0.7243 (ttpt) REVERT: D 185 ILE cc_start: 0.9093 (mt) cc_final: 0.8827 (tt) REVERT: D 195 ASP cc_start: 0.8286 (p0) cc_final: 0.8000 (p0) REVERT: D 271 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7389 (m) REVERT: D 310 LEU cc_start: 0.9008 (mt) cc_final: 0.8715 (mt) outliers start: 41 outliers final: 33 residues processed: 247 average time/residue: 0.2185 time to fit residues: 75.8327 Evaluate side-chains 231 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 0.0370 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN D 60 GLN D 136 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10672 Z= 0.160 Angle : 0.577 8.782 14464 Z= 0.292 Chirality : 0.040 0.167 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.064 16.744 1472 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.96 % Allowed : 19.24 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.44 (0.23), residues: 1364 helix: 2.23 (0.19), residues: 688 sheet: -0.63 (0.35), residues: 200 loop : -0.15 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 295 HIS 0.004 0.000 HIS B 237 PHE 0.033 0.001 PHE C 79 TYR 0.038 0.002 TYR C 222 ARG 0.007 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.7928 (ptm-80) cc_final: 0.7579 (ptm160) REVERT: B 79 PHE cc_start: 0.8844 (t80) cc_final: 0.8599 (t80) REVERT: B 127 LEU cc_start: 0.8516 (mt) cc_final: 0.7751 (pt) REVERT: B 206 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7937 (mm-30) REVERT: B 271 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7388 (m) REVERT: B 303 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7846 (mtp85) REVERT: B 326 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: A 119 ASN cc_start: 0.8656 (t0) cc_final: 0.8370 (t0) REVERT: A 127 LEU cc_start: 0.8928 (mt) cc_final: 0.8178 (pt) REVERT: A 189 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7171 (tt0) REVERT: A 206 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8256 (mm-30) REVERT: A 222 TYR cc_start: 0.8865 (t80) cc_final: 0.8496 (t80) REVERT: A 242 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8463 (tttm) REVERT: A 269 PHE cc_start: 0.8433 (m-80) cc_final: 0.8091 (m-80) REVERT: C 42 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7493 (mmm-85) REVERT: C 189 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7102 (tt0) REVERT: C 195 ASP cc_start: 0.7319 (t0) cc_final: 0.7014 (m-30) REVERT: C 222 TYR cc_start: 0.8549 (t80) cc_final: 0.8303 (t80) REVERT: C 242 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8491 (tttm) REVERT: C 269 PHE cc_start: 0.8378 (m-80) cc_final: 0.7684 (m-80) REVERT: D 100 LYS cc_start: 0.7649 (ptmt) cc_final: 0.7229 (ttpt) REVERT: D 271 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7339 (m) REVERT: D 325 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 329 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8501 (mmmt) outliers start: 44 outliers final: 36 residues processed: 247 average time/residue: 0.2309 time to fit residues: 79.9804 Evaluate side-chains 234 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN D 60 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.171 Angle : 0.581 8.422 14464 Z= 0.296 Chirality : 0.040 0.173 1644 Planarity : 0.004 0.027 1880 Dihedral : 4.074 16.778 1472 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.14 % Allowed : 20.23 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.49 (0.23), residues: 1364 helix: 2.27 (0.19), residues: 688 sheet: -0.56 (0.35), residues: 200 loop : -0.16 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 295 HIS 0.004 0.000 HIS B 237 PHE 0.028 0.002 PHE A 79 TYR 0.034 0.002 TYR C 222 ARG 0.007 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.7859 (ptm-80) cc_final: 0.7533 (ptm160) REVERT: B 79 PHE cc_start: 0.8850 (t80) cc_final: 0.8609 (t80) REVERT: B 206 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 271 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7376 (m) REVERT: B 303 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7849 (mtp180) REVERT: B 326 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: A 119 ASN cc_start: 0.8647 (t0) cc_final: 0.8343 (t0) REVERT: A 127 LEU cc_start: 0.8933 (mt) cc_final: 0.8161 (pt) REVERT: A 189 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7225 (tt0) REVERT: A 206 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 222 TYR cc_start: 0.8867 (t80) cc_final: 0.8432 (t80) REVERT: A 242 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8462 (tttm) REVERT: A 269 PHE cc_start: 0.8395 (m-80) cc_final: 0.8048 (m-80) REVERT: A 321 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7891 (tptp) REVERT: C 42 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7676 (mmm-85) REVERT: C 189 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7116 (tt0) REVERT: C 195 ASP cc_start: 0.7268 (t0) cc_final: 0.6915 (m-30) REVERT: C 242 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8530 (tttm) REVERT: C 269 PHE cc_start: 0.8355 (m-80) cc_final: 0.7733 (m-80) REVERT: C 325 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7996 (pp20) REVERT: D 58 TYR cc_start: 0.8217 (t80) cc_final: 0.8015 (t80) REVERT: D 100 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7238 (ttpt) REVERT: D 270 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7507 (mp) REVERT: D 271 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7336 (m) REVERT: D 325 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 329 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8490 (mmmt) outliers start: 46 outliers final: 36 residues processed: 247 average time/residue: 0.2322 time to fit residues: 80.3704 Evaluate side-chains 231 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.0570 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10672 Z= 0.163 Angle : 0.588 8.594 14464 Z= 0.300 Chirality : 0.040 0.164 1644 Planarity : 0.004 0.028 1880 Dihedral : 4.041 16.495 1472 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.97 % Allowed : 21.40 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.47 (0.23), residues: 1364 helix: 2.21 (0.19), residues: 688 sheet: -0.53 (0.35), residues: 200 loop : -0.11 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.005 0.000 HIS B 237 PHE 0.009 0.001 PHE A 144 TYR 0.043 0.002 TYR C 222 ARG 0.006 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.7884 (ptm-80) cc_final: 0.7618 (ptm160) REVERT: B 79 PHE cc_start: 0.8817 (t80) cc_final: 0.8607 (t80) REVERT: B 127 LEU cc_start: 0.8540 (mt) cc_final: 0.7758 (pt) REVERT: B 206 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 271 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7311 (m) REVERT: B 303 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7828 (mtp180) REVERT: A 119 ASN cc_start: 0.8618 (t0) cc_final: 0.8330 (t0) REVERT: A 127 LEU cc_start: 0.8899 (mt) cc_final: 0.8122 (pt) REVERT: A 189 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7244 (tt0) REVERT: A 195 ASP cc_start: 0.7318 (t0) cc_final: 0.7033 (m-30) REVERT: A 222 TYR cc_start: 0.8853 (t80) cc_final: 0.8366 (t80) REVERT: A 242 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8467 (tttm) REVERT: A 269 PHE cc_start: 0.8391 (m-80) cc_final: 0.7999 (m-80) REVERT: A 321 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7892 (tptp) REVERT: C 189 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7154 (tt0) REVERT: C 195 ASP cc_start: 0.7288 (t0) cc_final: 0.6879 (m-30) REVERT: C 242 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8546 (tttm) REVERT: C 269 PHE cc_start: 0.8236 (m-80) cc_final: 0.7731 (m-80) REVERT: C 303 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7418 (ttm-80) REVERT: C 325 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8018 (pp20) REVERT: D 271 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7312 (m) outliers start: 33 outliers final: 29 residues processed: 242 average time/residue: 0.2206 time to fit residues: 74.9422 Evaluate side-chains 230 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.205 Angle : 0.623 8.671 14464 Z= 0.316 Chirality : 0.041 0.180 1644 Planarity : 0.004 0.034 1880 Dihedral : 4.144 20.701 1472 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.33 % Allowed : 21.49 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.58 (0.23), residues: 1364 helix: 2.28 (0.19), residues: 688 sheet: 0.07 (0.39), residues: 156 loop : -0.30 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 295 HIS 0.005 0.001 HIS D 237 PHE 0.027 0.002 PHE A 79 TYR 0.044 0.003 TYR C 222 ARG 0.006 0.000 ARG A 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7337 (ptm-80) REVERT: B 79 PHE cc_start: 0.8874 (t80) cc_final: 0.8651 (t80) REVERT: B 127 LEU cc_start: 0.8700 (mt) cc_final: 0.7805 (pt) REVERT: B 206 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 271 SER cc_start: 0.7740 (OUTLIER) cc_final: 0.7336 (m) REVERT: B 303 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7861 (mtp180) REVERT: A 119 ASN cc_start: 0.8637 (t0) cc_final: 0.8347 (t0) REVERT: A 206 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7974 (mm-30) REVERT: A 242 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8450 (tttm) REVERT: A 269 PHE cc_start: 0.8446 (m-80) cc_final: 0.8111 (m-80) REVERT: A 321 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7859 (tptp) REVERT: C 127 LEU cc_start: 0.8946 (mt) cc_final: 0.8002 (pt) REVERT: C 189 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7158 (tt0) REVERT: C 195 ASP cc_start: 0.7303 (t0) cc_final: 0.6943 (m-30) REVERT: C 206 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 242 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8554 (tttm) REVERT: C 269 PHE cc_start: 0.8322 (m-80) cc_final: 0.7842 (m-80) REVERT: C 301 TYR cc_start: 0.7700 (m-80) cc_final: 0.7403 (m-80) REVERT: C 303 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7530 (mtp180) REVERT: C 321 LYS cc_start: 0.8525 (mmmt) cc_final: 0.7939 (tptp) REVERT: C 325 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7959 (pp20) REVERT: D 271 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7331 (m) outliers start: 37 outliers final: 32 residues processed: 235 average time/residue: 0.2077 time to fit residues: 69.8094 Evaluate side-chains 228 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 136 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094016 restraints weight = 21972.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096991 restraints weight = 12583.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098954 restraints weight = 8722.693| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.177 Angle : 0.607 8.536 14464 Z= 0.310 Chirality : 0.041 0.165 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.067 18.469 1472 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.51 % Allowed : 21.49 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1364 helix: 2.24 (0.19), residues: 688 sheet: -0.11 (0.38), residues: 176 loop : -0.17 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 295 HIS 0.005 0.001 HIS D 237 PHE 0.014 0.001 PHE C 93 TYR 0.038 0.003 TYR C 222 ARG 0.006 0.000 ARG A 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.25 seconds wall clock time: 45 minutes 12.56 seconds (2712.56 seconds total)