Starting phenix.real_space_refine on Sat Jul 20 21:51:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f35_28832/07_2024/8f35_28832.cif" } resolution = 3.17 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= 0.014 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 30 5.16 5 C 8165 2.51 5 N 2080 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12525 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Time building chain proxies: 7.32, per 1000 atoms: 0.58 Number of scatterers: 12525 At special positions: 0 Unit cell: (89.352, 90.009, 123.516, 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 30 16.00 O 2250 8.00 N 2080 7.00 C 8165 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: 4.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 38.1% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'E' and resid 61 through 70 removed outlier: 3.875A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL E 181 " --> pdb=" O HIS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 removed outlier: 3.654A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.502A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.556A pdb=" N ILE E 317 " --> pdb=" O CYS E 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.876A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL D 181 " --> pdb=" O HIS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.503A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.874A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.501A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.556A pdb=" N ILE C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.875A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.502A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.876A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.503A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 26 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 22 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 26 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 22 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.688A pdb=" N THR C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 26 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 22 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 26 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 22 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 26 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 22 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3131 1.33 - 1.45: 2671 1.45 - 1.57: 7013 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12865 Sorted by residual: bond pdb=" CA ILE C 157 " pdb=" C ILE C 157 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.27e-02 6.20e+03 5.17e+00 bond pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.86e+00 bond pdb=" CA ILE D 157 " pdb=" C ILE D 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.77e+00 bond pdb=" CA ILE E 157 " pdb=" C ILE E 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.72e+00 bond pdb=" CA ILE B 157 " pdb=" C ILE B 157 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.27e-02 6.20e+03 4.61e+00 ... (remaining 12860 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 541 107.50 - 114.13: 7061 114.13 - 120.75: 5397 120.75 - 127.37: 4377 127.37 - 134.00: 159 Bond angle restraints: 17535 Sorted by residual: angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.53 109.61 3.92 9.80e-01 1.04e+00 1.60e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.53 109.63 3.90 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.53 109.66 3.87 9.80e-01 1.04e+00 1.56e+01 ... (remaining 17530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 6727 16.75 - 33.51: 618 33.51 - 50.26: 130 50.26 - 67.02: 25 67.02 - 83.77: 25 Dihedral angle restraints: 7525 sinusoidal: 3020 harmonic: 4505 Sorted by residual: dihedral pdb=" CA ARG A 117 " pdb=" C ARG A 117 " pdb=" N LEU A 118 " pdb=" CA LEU A 118 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ARG D 117 " pdb=" C ARG D 117 " pdb=" N LEU D 118 " pdb=" CA LEU D 118 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ARG B 117 " pdb=" C ARG B 117 " pdb=" N LEU B 118 " pdb=" CA LEU B 118 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1003 0.032 - 0.065: 578 0.065 - 0.097: 200 0.097 - 0.129: 143 0.129 - 0.161: 26 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE D 145 " pdb=" CA ILE D 145 " pdb=" CG1 ILE D 145 " pdb=" CG2 ILE D 145 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB ILE E 145 " pdb=" CA ILE E 145 " pdb=" CG1 ILE E 145 " pdb=" CG2 ILE E 145 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 255 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG B 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG B 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 256 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 255 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ARG D 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG D 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 256 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 255 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ARG E 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG E 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 256 " -0.013 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2156 2.77 - 3.30: 11455 3.30 - 3.83: 21643 3.83 - 4.37: 25522 4.37 - 4.90: 43725 Nonbonded interactions: 104501 Sorted by model distance: nonbonded pdb=" NH2 ARG E 105 " pdb=" O VAL D 81 " model vdw 2.235 2.520 nonbonded pdb=" N PHE C 116 " pdb=" OH TYR C 258 " model vdw 2.243 2.520 nonbonded pdb=" N PHE E 116 " pdb=" OH TYR E 258 " model vdw 2.243 2.520 nonbonded pdb=" N PHE D 116 " pdb=" OH TYR D 258 " model vdw 2.243 2.520 nonbonded pdb=" N PHE B 116 " pdb=" OH TYR B 258 " model vdw 2.243 2.520 ... (remaining 104496 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' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 35.600 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.005 0.042 12865 Z= 0.317 Angle : 0.746 6.643 17535 Z= 0.428 Chirality : 0.051 0.161 1950 Planarity : 0.005 0.037 2235 Dihedral : 14.231 83.771 4615 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1525 helix: 0.08 (0.22), residues: 510 sheet: 0.45 (0.23), residues: 485 loop : -2.55 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 72 HIS 0.008 0.002 HIS A 285 PHE 0.017 0.002 PHE C 236 TYR 0.020 0.002 TYR C 270 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.348 Fit side-chains REVERT: D 13 ASP cc_start: 0.6885 (m-30) cc_final: 0.6428 (m-30) REVERT: C 122 ASP cc_start: 0.7345 (m-30) cc_final: 0.6954 (m-30) REVERT: A 204 TYR cc_start: 0.8073 (m-80) cc_final: 0.7700 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2473 time to fit residues: 81.3457 Evaluate side-chains 188 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 0.0170 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN D 60 ASN D 169 HIS C 60 ASN C 169 HIS B 60 ASN B 169 HIS A 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12865 Z= 0.191 Angle : 0.490 4.953 17535 Z= 0.262 Chirality : 0.044 0.160 1950 Planarity : 0.004 0.030 2235 Dihedral : 4.504 17.516 1685 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.73 % Allowed : 7.05 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1525 helix: 1.31 (0.23), residues: 510 sheet: 0.37 (0.23), residues: 500 loop : -2.23 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.004 0.001 HIS E 285 PHE 0.013 0.001 PHE C 236 TYR 0.012 0.001 TYR A 270 ARG 0.002 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 205 time to evaluate : 1.455 Fit side-chains REVERT: E 114 MET cc_start: 0.8482 (mtm) cc_final: 0.8267 (mtp) REVERT: D 13 ASP cc_start: 0.6896 (m-30) cc_final: 0.6648 (m-30) REVERT: D 251 ASN cc_start: 0.7874 (t0) cc_final: 0.7636 (t0) REVERT: C 114 MET cc_start: 0.8452 (mtm) cc_final: 0.8179 (mtp) REVERT: A 114 MET cc_start: 0.8455 (mtm) cc_final: 0.8203 (mtp) outliers start: 10 outliers final: 7 residues processed: 210 average time/residue: 0.2490 time to fit residues: 75.4933 Evaluate side-chains 191 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 169 HIS B 169 HIS A 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12865 Z= 0.427 Angle : 0.652 6.987 17535 Z= 0.342 Chirality : 0.050 0.186 1950 Planarity : 0.005 0.032 2235 Dihedral : 5.353 19.977 1685 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.89 % Allowed : 10.76 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1525 helix: 1.20 (0.23), residues: 510 sheet: 0.34 (0.23), residues: 485 loop : -2.14 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 206 HIS 0.004 0.001 HIS E 285 PHE 0.024 0.002 PHE C 236 TYR 0.014 0.002 TYR B 270 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.464 Fit side-chains REVERT: B 159 GLU cc_start: 0.7706 (tt0) cc_final: 0.7503 (tt0) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.2525 time to fit residues: 55.3914 Evaluate side-chains 152 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 219 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12865 Z= 0.150 Angle : 0.467 4.897 17535 Z= 0.246 Chirality : 0.044 0.132 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.474 14.888 1685 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.02 % Allowed : 13.09 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1525 helix: 1.85 (0.23), residues: 510 sheet: 0.35 (0.24), residues: 480 loop : -2.06 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 161 HIS 0.003 0.001 HIS E 285 PHE 0.014 0.001 PHE C 236 TYR 0.010 0.001 TYR A 245 ARG 0.002 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.411 Fit side-chains REVERT: E 114 MET cc_start: 0.8501 (mtm) cc_final: 0.8223 (mtp) REVERT: C 114 MET cc_start: 0.8436 (mtm) cc_final: 0.8165 (mtp) REVERT: B 266 ILE cc_start: 0.8426 (mm) cc_final: 0.8218 (mt) REVERT: A 114 MET cc_start: 0.8475 (mtm) cc_final: 0.8193 (mtp) outliers start: 14 outliers final: 11 residues processed: 172 average time/residue: 0.2754 time to fit residues: 66.1649 Evaluate side-chains 162 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS B 169 HIS A 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12865 Z= 0.442 Angle : 0.644 6.054 17535 Z= 0.337 Chirality : 0.049 0.209 1950 Planarity : 0.004 0.029 2235 Dihedral : 5.232 19.853 1685 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.11 % Allowed : 14.55 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1525 helix: 1.48 (0.23), residues: 505 sheet: 0.24 (0.23), residues: 485 loop : -2.12 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 161 HIS 0.005 0.001 HIS B 285 PHE 0.014 0.002 PHE D 282 TYR 0.014 0.002 TYR B 270 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.425 Fit side-chains outliers start: 29 outliers final: 26 residues processed: 149 average time/residue: 0.2513 time to fit residues: 53.8778 Evaluate side-chains 158 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 219 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12865 Z= 0.146 Angle : 0.463 4.913 17535 Z= 0.244 Chirality : 0.044 0.162 1950 Planarity : 0.003 0.027 2235 Dihedral : 4.403 15.459 1685 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.45 % Allowed : 15.56 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1525 helix: 1.53 (0.23), residues: 540 sheet: 0.39 (0.24), residues: 450 loop : -1.98 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 161 HIS 0.003 0.001 HIS E 285 PHE 0.008 0.001 PHE D 282 TYR 0.010 0.001 TYR E 148 ARG 0.002 0.000 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.424 Fit side-chains REVERT: D 93 MET cc_start: 0.7730 (ttm) cc_final: 0.7463 (mmm) REVERT: A 114 MET cc_start: 0.8475 (mtm) cc_final: 0.8194 (mtp) outliers start: 20 outliers final: 16 residues processed: 159 average time/residue: 0.2844 time to fit residues: 63.1694 Evaluate side-chains 159 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12865 Z= 0.248 Angle : 0.523 5.350 17535 Z= 0.273 Chirality : 0.046 0.204 1950 Planarity : 0.003 0.025 2235 Dihedral : 4.648 16.406 1685 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.89 % Allowed : 15.42 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1525 helix: 1.93 (0.23), residues: 505 sheet: 0.34 (0.23), residues: 485 loop : -1.91 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 161 HIS 0.004 0.001 HIS B 285 PHE 0.011 0.002 PHE A 304 TYR 0.012 0.001 TYR C 270 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.431 Fit side-chains REVERT: E 114 MET cc_start: 0.8608 (mtm) cc_final: 0.8399 (mtp) REVERT: E 149 THR cc_start: 0.8038 (t) cc_final: 0.7604 (p) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.2553 time to fit residues: 57.6169 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.0010 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12865 Z= 0.154 Angle : 0.466 4.911 17535 Z= 0.244 Chirality : 0.044 0.182 1950 Planarity : 0.003 0.023 2235 Dihedral : 4.349 15.841 1685 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.38 % Allowed : 16.00 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1525 helix: 2.01 (0.23), residues: 510 sheet: 0.37 (0.23), residues: 490 loop : -1.88 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 161 HIS 0.004 0.001 HIS B 285 PHE 0.009 0.001 PHE D 282 TYR 0.010 0.001 TYR A 245 ARG 0.005 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.388 Fit side-chains REVERT: E 114 MET cc_start: 0.8539 (mtm) cc_final: 0.8257 (mtp) REVERT: E 115 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (p0) REVERT: D 93 MET cc_start: 0.7716 (ttm) cc_final: 0.7418 (mmm) REVERT: D 122 ASP cc_start: 0.8068 (m-30) cc_final: 0.7839 (m-30) REVERT: C 97 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6623 (p0) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.2622 time to fit residues: 58.3404 Evaluate side-chains 158 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 12865 Z= 0.427 Angle : 0.640 6.563 17535 Z= 0.334 Chirality : 0.049 0.183 1950 Planarity : 0.004 0.027 2235 Dihedral : 5.158 19.160 1685 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.04 % Allowed : 15.93 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1525 helix: 1.50 (0.23), residues: 505 sheet: 0.18 (0.23), residues: 485 loop : -1.99 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 161 HIS 0.005 0.001 HIS C 285 PHE 0.014 0.002 PHE A 304 TYR 0.013 0.002 TYR C 270 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.361 Fit side-chains REVERT: E 149 THR cc_start: 0.8021 (t) cc_final: 0.7656 (p) REVERT: C 149 THR cc_start: 0.8145 (t) cc_final: 0.7800 (p) outliers start: 28 outliers final: 25 residues processed: 153 average time/residue: 0.2781 time to fit residues: 60.7323 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0570 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12865 Z= 0.159 Angle : 0.471 4.894 17535 Z= 0.248 Chirality : 0.044 0.174 1950 Planarity : 0.003 0.023 2235 Dihedral : 4.452 15.830 1685 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.24 % Allowed : 16.87 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1525 helix: 1.92 (0.23), residues: 510 sheet: 0.24 (0.23), residues: 495 loop : -1.77 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 161 HIS 0.005 0.001 HIS B 285 PHE 0.008 0.001 PHE E 247 TYR 0.011 0.001 TYR A 245 ARG 0.003 0.000 ARG B 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.364 Fit side-chains REVERT: D 93 MET cc_start: 0.7707 (ttm) cc_final: 0.7451 (mmm) REVERT: C 97 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6582 (p0) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 0.2675 time to fit residues: 55.8405 Evaluate side-chains 151 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 33 optimal weight: 0.2980 chunk 119 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 2.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS ** A 251 ASN ** 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 = 0.3567 r_free = 0.3567 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.122051 restraints weight = 13144.087| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.43 r_work: 0.2988 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12865 Z= 0.258 Angle : 0.529 5.418 17535 Z= 0.277 Chirality : 0.046 0.175 1950 Planarity : 0.003 0.024 2235 Dihedral : 4.686 16.409 1685 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.75 % Allowed : 16.65 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1525 helix: 1.90 (0.23), residues: 505 sheet: 0.23 (0.23), residues: 490 loop : -1.78 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 161 HIS 0.004 0.001 HIS C 285 PHE 0.011 0.002 PHE A 304 TYR 0.011 0.001 TYR C 270 ARG 0.002 0.000 ARG C 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.73 seconds wall clock time: 46 minutes 5.92 seconds (2765.92 seconds total)