Starting phenix.real_space_refine on Fri Mar 15 03:31:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka2_22756/03_2024/7ka2_22756.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-5265/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: 6.19, per 1000 atoms: 0.59 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: 4.18 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: 1.27 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: 2.97 Time building geometry restraints manager: 4.52 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.310 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.340 Find NCS groups from input model: 0.620 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 402 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 334 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.8742 (tpp) cc_final: 0.8428 (tpt) REVERT: A 233 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.6805 (p) REVERT: A 250 MET cc_start: 0.8667 (tpp) cc_final: 0.8419 (tpt) REVERT: A 271 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 301 TYR cc_start: 0.7412 (m-10) cc_final: 0.7003 (m-10) REVERT: C 39 ILE cc_start: 0.9263 (tp) cc_final: 0.8931 (tp) REVERT: C 60 GLN cc_start: 0.8489 (mt0) cc_final: 0.7667 (mt0) REVERT: C 250 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpt) REVERT: C 271 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 301 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-10) outliers start: 68 outliers final: 6 residues processed: 373 average time/residue: 0.2627 time to fit residues: 130.7558 Evaluate side-chains 195 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 60 GLN B 80 HIS B 125 GLN B 287 ASN A 125 GLN A 168 ASN A 287 ASN C 80 HIS C 125 GLN C 287 ASN D 44 GLN D 54 ASN D 287 ASN D 334 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.188 Angle : 0.616 8.696 14464 Z= 0.318 Chirality : 0.042 0.167 1644 Planarity : 0.004 0.032 1880 Dihedral : 4.880 30.545 1481 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.06 % Allowed : 15.38 % Favored : 81.56 % 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: 0.06 (0.22), residues: 1364 helix: 0.90 (0.18), residues: 684 sheet: -1.50 (0.33), residues: 204 loop : -0.32 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 147 HIS 0.003 0.001 HIS B 245 PHE 0.014 0.002 PHE B 93 TYR 0.019 0.002 TYR C 203 ARG 0.004 0.000 ARG D 59 *********************** 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 270 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.7794 (tp30) cc_final: 0.7385 (tp30) REVERT: B 316 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8749 (mmtm) REVERT: B 330 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8045 (ttp-170) REVERT: A 82 THR cc_start: 0.9044 (m) cc_final: 0.8821 (m) REVERT: A 250 MET cc_start: 0.8703 (tpp) cc_final: 0.8495 (tpt) REVERT: C 250 MET cc_start: 0.8798 (tpp) cc_final: 0.8570 (tpt) outliers start: 34 outliers final: 18 residues processed: 252 average time/residue: 0.2242 time to fit residues: 78.7545 Evaluate side-chains 189 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.0170 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 chunk 99 optimal weight: 3.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS B 85 GLN A 60 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 85 GLN D 60 GLN D 80 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10672 Z= 0.164 Angle : 0.582 8.340 14464 Z= 0.296 Chirality : 0.041 0.165 1644 Planarity : 0.004 0.061 1880 Dihedral : 4.278 17.664 1472 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.43 % Allowed : 17.27 % Favored : 80.31 % 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: 0.85 (0.23), residues: 1364 helix: 1.68 (0.20), residues: 676 sheet: -0.92 (0.35), residues: 188 loop : -0.30 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 313 HIS 0.003 0.000 HIS D 245 PHE 0.018 0.002 PHE B 93 TYR 0.014 0.002 TYR C 203 ARG 0.005 0.000 ARG D 59 *********************** 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 233 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8273 (p) cc_final: 0.7946 (p) REVERT: B 330 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8411 (ttp-170) REVERT: A 250 MET cc_start: 0.8639 (tpp) cc_final: 0.8434 (tpt) REVERT: C 330 ARG cc_start: 0.9056 (mmm160) cc_final: 0.8845 (ttp-170) outliers start: 27 outliers final: 18 residues processed: 220 average time/residue: 0.2179 time to fit residues: 68.6142 Evaluate side-chains 183 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 339 GLN Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 80 HIS C 85 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 85 GLN ** 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: 0.8350 moved from start: 0.3926 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= 0.185 Angle : 0.588 7.519 14464 Z= 0.300 Chirality : 0.041 0.170 1644 Planarity : 0.004 0.048 1880 Dihedral : 4.150 18.692 1472 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.79 % Allowed : 19.06 % Favored : 78.15 % 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: 1.01 (0.23), residues: 1364 helix: 1.84 (0.20), residues: 680 sheet: -0.66 (0.35), residues: 184 loop : -0.38 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 313 HIS 0.007 0.001 HIS C 80 PHE 0.011 0.001 PHE A 93 TYR 0.018 0.002 TYR C 203 ARG 0.004 0.000 ARG D 59 *********************** 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 214 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8276 (p) cc_final: 0.7967 (p) REVERT: B 218 ASP cc_start: 0.8612 (t0) cc_final: 0.8163 (t0) REVERT: A 250 MET cc_start: 0.8648 (tpp) cc_final: 0.8434 (tpt) REVERT: A 252 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8124 (p) REVERT: C 330 ARG cc_start: 0.9049 (mmm160) cc_final: 0.8818 (ttp-170) REVERT: D 164 MET cc_start: 0.8506 (tmm) cc_final: 0.8263 (ptt) outliers start: 31 outliers final: 23 residues processed: 199 average time/residue: 0.1842 time to fit residues: 54.1033 Evaluate side-chains 186 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 339 GLN Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 overall best weight: 0.5148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4161 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= 0.162 Angle : 0.564 7.775 14464 Z= 0.286 Chirality : 0.041 0.150 1644 Planarity : 0.004 0.044 1880 Dihedral : 3.996 16.333 1472 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.24 % Allowed : 18.97 % Favored : 77.79 % 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: 1.14 (0.23), residues: 1364 helix: 2.08 (0.19), residues: 676 sheet: -0.64 (0.35), residues: 184 loop : -0.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 313 HIS 0.011 0.000 HIS C 80 PHE 0.018 0.002 PHE B 79 TYR 0.019 0.001 TYR B 203 ARG 0.003 0.000 ARG D 59 *********************** 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 215 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8250 (p) cc_final: 0.7868 (p) REVERT: B 330 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8356 (ttm170) REVERT: A 124 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 250 MET cc_start: 0.8638 (tpp) cc_final: 0.8427 (tpt) REVERT: C 252 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 325 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8703 (pp20) REVERT: C 330 ARG cc_start: 0.9057 (mmm160) cc_final: 0.8835 (ttp-170) REVERT: D 229 LYS cc_start: 0.9144 (tttt) cc_final: 0.8927 (tptm) outliers start: 36 outliers final: 23 residues processed: 196 average time/residue: 0.2086 time to fit residues: 58.7539 Evaluate side-chains 188 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 339 GLN 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: 0.9980 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10672 Z= 0.168 Angle : 0.565 10.547 14464 Z= 0.285 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.050 1880 Dihedral : 3.921 17.565 1472 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.78 % Allowed : 19.24 % Favored : 76.98 % 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: 1.15 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 676 sheet: -1.02 (0.33), residues: 208 loop : -0.29 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 313 HIS 0.008 0.000 HIS A 80 PHE 0.019 0.001 PHE B 79 TYR 0.019 0.001 TYR B 137 ARG 0.003 0.000 ARG C 56 *********************** 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 214 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8258 (p) cc_final: 0.7869 (p) REVERT: B 330 ARG cc_start: 0.9000 (mmm160) cc_final: 0.8548 (ttp-170) REVERT: A 124 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8793 (m) REVERT: A 250 MET cc_start: 0.8656 (tpp) cc_final: 0.8454 (tpt) REVERT: D 229 LYS cc_start: 0.9146 (tttt) cc_final: 0.8935 (tptm) REVERT: D 330 ARG cc_start: 0.9118 (mmm160) cc_final: 0.8644 (ttp-170) outliers start: 42 outliers final: 28 residues processed: 197 average time/residue: 0.2094 time to fit residues: 59.0027 Evaluate side-chains 186 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 326 GLU 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: 2.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10672 Z= 0.292 Angle : 0.623 8.737 14464 Z= 0.317 Chirality : 0.042 0.152 1644 Planarity : 0.004 0.052 1880 Dihedral : 4.054 17.031 1472 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.69 % Allowed : 19.87 % Favored : 76.44 % 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: 1.14 (0.23), residues: 1364 helix: 1.99 (0.19), residues: 692 sheet: -0.99 (0.33), residues: 208 loop : -0.21 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 313 HIS 0.006 0.001 HIS B 80 PHE 0.020 0.001 PHE B 79 TYR 0.037 0.002 TYR B 137 ARG 0.002 0.000 ARG B 172 *********************** 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 198 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.9025 (t80) cc_final: 0.8796 (t80) REVERT: B 134 CYS cc_start: 0.8290 (p) cc_final: 0.8088 (p) REVERT: B 330 ARG cc_start: 0.9051 (mmm160) cc_final: 0.8642 (ttp-170) REVERT: A 124 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8853 (m) REVERT: A 250 MET cc_start: 0.8684 (tpp) cc_final: 0.8477 (tpt) REVERT: D 330 ARG cc_start: 0.9105 (mmm160) cc_final: 0.8396 (mtm180) outliers start: 41 outliers final: 29 residues processed: 182 average time/residue: 0.2128 time to fit residues: 55.3526 Evaluate side-chains 179 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 343 THR 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.192 Angle : 0.602 8.684 14464 Z= 0.302 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.052 1880 Dihedral : 4.004 18.255 1472 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.22 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 684 sheet: -1.12 (0.32), residues: 220 loop : -0.10 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 313 HIS 0.013 0.001 HIS A 80 PHE 0.020 0.001 PHE B 79 TYR 0.049 0.002 TYR B 137 ARG 0.004 0.000 ARG C 330 *********************** 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 190 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8312 (p) cc_final: 0.8017 (p) REVERT: B 330 ARG cc_start: 0.9043 (mmm160) cc_final: 0.8598 (ttp-170) REVERT: A 250 MET cc_start: 0.8664 (tpp) cc_final: 0.8447 (tpt) REVERT: C 252 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 321 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8542 (mmmt) REVERT: D 23 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8021 (m) REVERT: D 134 CYS cc_start: 0.8230 (p) cc_final: 0.7701 (p) outliers start: 33 outliers final: 24 residues processed: 179 average time/residue: 0.2181 time to fit residues: 55.9865 Evaluate side-chains 171 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 326 GLU 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: 3.9990 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 0.0470 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN A 80 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 80 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.182 Angle : 0.621 9.567 14464 Z= 0.309 Chirality : 0.041 0.146 1644 Planarity : 0.004 0.058 1880 Dihedral : 3.970 17.069 1472 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.15 % Allowed : 22.03 % Favored : 74.82 % 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: 1.21 (0.23), residues: 1364 helix: 2.15 (0.19), residues: 680 sheet: -0.98 (0.33), residues: 208 loop : -0.27 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 313 HIS 0.005 0.000 HIS D 80 PHE 0.021 0.001 PHE B 79 TYR 0.053 0.002 TYR B 137 ARG 0.003 0.000 ARG A 56 *********************** 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 188 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.7917 (m) REVERT: B 134 CYS cc_start: 0.8280 (p) cc_final: 0.7909 (p) REVERT: B 330 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8621 (ttp-170) REVERT: A 250 MET cc_start: 0.8666 (tpp) cc_final: 0.8446 (tpt) REVERT: D 23 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7965 (m) REVERT: D 134 CYS cc_start: 0.8224 (p) cc_final: 0.7683 (p) REVERT: D 164 MET cc_start: 0.8571 (tmm) cc_final: 0.8326 (ptt) REVERT: D 229 LYS cc_start: 0.9247 (tttt) cc_final: 0.9045 (tptm) outliers start: 35 outliers final: 23 residues processed: 177 average time/residue: 0.2010 time to fit residues: 51.9629 Evaluate side-chains 171 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 326 GLU 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 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 80 HIS B 334 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10672 Z= 0.180 Angle : 0.625 7.999 14464 Z= 0.312 Chirality : 0.041 0.154 1644 Planarity : 0.004 0.092 1880 Dihedral : 3.949 17.549 1472 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.52 % Allowed : 22.66 % Favored : 74.82 % 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: 2.17 (0.19), residues: 680 sheet: -0.96 (0.34), residues: 208 loop : -0.25 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 313 HIS 0.007 0.000 HIS D 80 PHE 0.036 0.002 PHE B 79 TYR 0.050 0.002 TYR B 137 ARG 0.003 0.000 ARG C 56 ********************** 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 182 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7924 (m) REVERT: B 134 CYS cc_start: 0.8271 (p) cc_final: 0.7882 (p) REVERT: B 330 ARG cc_start: 0.9049 (mmm160) cc_final: 0.8604 (ttp-170) REVERT: A 250 MET cc_start: 0.8664 (tpp) cc_final: 0.8446 (tpt) REVERT: A 311 LYS cc_start: 0.9602 (ptmm) cc_final: 0.9362 (ptmm) REVERT: D 44 GLN cc_start: 0.8552 (mm110) cc_final: 0.8341 (mm-40) REVERT: D 134 CYS cc_start: 0.8225 (p) cc_final: 0.7680 (p) REVERT: D 164 MET cc_start: 0.8558 (tmm) cc_final: 0.8319 (ptt) REVERT: D 229 LYS cc_start: 0.9252 (tttt) cc_final: 0.9050 (tptm) REVERT: D 330 ARG cc_start: 0.9082 (mmm160) cc_final: 0.8675 (ttp-170) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.2071 time to fit residues: 52.6010 Evaluate side-chains 175 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 326 GLU 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: 9.9990 chunk 99 optimal weight: 0.1980 chunk 15 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.095603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074010 restraints weight = 29077.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076452 restraints weight = 16368.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077963 restraints weight = 11307.254| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10672 Z= 0.169 Angle : 0.623 8.249 14464 Z= 0.311 Chirality : 0.042 0.215 1644 Planarity : 0.004 0.087 1880 Dihedral : 3.901 17.847 1472 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.43 % Allowed : 23.20 % Favored : 74.37 % 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: 1.19 (0.23), residues: 1364 helix: 2.13 (0.19), residues: 680 sheet: -0.74 (0.31), residues: 256 loop : -0.34 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 313 HIS 0.002 0.000 HIS A 219 PHE 0.023 0.001 PHE A 79 TYR 0.048 0.002 TYR B 137 ARG 0.003 0.000 ARG C 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.09 seconds wall clock time: 42 minutes 24.90 seconds (2544.90 seconds total)