Starting phenix.real_space_refine on Fri May 10 02:46:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/05_2024/8v2z_42938_updated.pdb" } resolution = 2.72 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9230 2.51 5 N 2455 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14635 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.96, per 1000 atoms: 0.54 Number of scatterers: 14635 At special positions: 0 Unit cell: (105.93, 77.04, 193.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2455 7.00 C 9230 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: 5.81 Conformation dependent library (CDL) restraints added in 2.6 seconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 20 sheets defined 40.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.276A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.909A pdb=" N CYS A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.917A pdb=" N CYS B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.939A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 removed outlier: 4.192A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.731A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.540A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.940A pdb=" N CYS C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 removed outlier: 4.207A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 192 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.949A pdb=" N CYS D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.147A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.053A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.838A pdb=" N CYS E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.950A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.161A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.713A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.381A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.820A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.428A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.758A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.452A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.815A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.388A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.813A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.383A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 509 hydrogen bonds defined for protein. 1356 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: 4.32 Time building geometry restraints manager: 6.26 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: 4707 1.34 - 1.46: 3390 1.46 - 1.58: 6662 1.58 - 1.70: 16 1.70 - 1.83: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.34: 375 105.34 - 113.06: 8036 113.06 - 120.77: 6979 120.77 - 128.49: 4820 128.49 - 136.20: 100 Bond angle restraints: 20310 Sorted by residual: angle pdb=" CA PRO C 367 " pdb=" N PRO C 367 " pdb=" CD PRO C 367 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.75e+01 angle pdb=" CA PRO E 367 " pdb=" N PRO E 367 " pdb=" CD PRO E 367 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CB MET B 227 " pdb=" CG MET B 227 " pdb=" SD MET B 227 " ideal model delta sigma weight residual 112.70 127.32 -14.62 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " pdb=" CD GLN A 354 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.70e+00 3.46e-01 2.19e+01 angle pdb=" CA GLN A 354 " pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 20305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 8394 24.54 - 49.07: 545 49.07 - 73.61: 53 73.61 - 98.14: 3 98.14 - 122.68: 5 Dihedral angle restraints: 9000 sinusoidal: 3625 harmonic: 5375 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.32 122.68 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -173.21 113.21 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.01 112.00 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1982 0.082 - 0.164: 260 0.164 - 0.247: 3 0.247 - 0.329: 3 0.329 - 0.411: 2 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2247 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " 0.133 5.00e-02 4.00e+02 1.91e-01 5.85e+01 pdb=" N PRO C 367 " -0.330 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 366 " 0.108 5.00e-02 4.00e+02 1.60e-01 4.12e+01 pdb=" N PRO E 367 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO E 367 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO E 367 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO D 367 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.040 5.00e-02 4.00e+02 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 811 2.73 - 3.27: 13391 3.27 - 3.81: 24817 3.81 - 4.36: 31918 4.36 - 4.90: 52829 Nonbonded interactions: 123766 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.237 2.170 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.272 2.440 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.273 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.280 2.440 ... (remaining 123761 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: 1.040 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: 4.390 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 42.290 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 0.116 14960 Z= 0.309 Angle : 0.777 14.616 20310 Z= 0.399 Chirality : 0.052 0.411 2250 Planarity : 0.008 0.191 2600 Dihedral : 15.424 122.676 5560 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.51 % Allowed : 17.52 % Favored : 81.97 % 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: -1.04 (0.19), residues: 1835 helix: -1.57 (0.16), residues: 730 sheet: 0.41 (0.28), residues: 355 loop : -0.04 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.022 0.002 PHE C 127 TYR 0.008 0.001 TYR C 362 ARG 0.005 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.128 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 1.8608 time to fit residues: 201.4628 Evaluate side-chains 95 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14960 Z= 0.323 Angle : 0.575 6.971 20310 Z= 0.269 Chirality : 0.045 0.154 2250 Planarity : 0.005 0.115 2600 Dihedral : 7.629 103.245 2094 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 15.80 % 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: 0.05 (0.20), residues: 1835 helix: -0.25 (0.19), residues: 740 sheet: 0.57 (0.28), residues: 340 loop : 0.33 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE C 255 TYR 0.009 0.001 TYR B 188 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 1.706 Fit side-chains REVERT: A 314 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: B 176 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: B 354 GLN cc_start: 0.8708 (pp30) cc_final: 0.8147 (pp30) REVERT: C 325 MET cc_start: 0.8707 (mmp) cc_final: 0.8402 (mmp) outliers start: 34 outliers final: 3 residues processed: 112 average time/residue: 1.8219 time to fit residues: 220.1972 Evaluate side-chains 95 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14960 Z= 0.305 Angle : 0.557 7.003 20310 Z= 0.259 Chirality : 0.045 0.163 2250 Planarity : 0.004 0.091 2600 Dihedral : 7.393 101.218 2087 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.97 % Allowed : 15.80 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1835 helix: 0.43 (0.20), residues: 740 sheet: 0.89 (0.30), residues: 315 loop : 0.44 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE E 255 TYR 0.007 0.001 TYR B 188 ARG 0.001 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.814 Fit side-chains REVERT: A 314 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: A 354 GLN cc_start: 0.8694 (pp30) cc_final: 0.8439 (pp30) REVERT: A 355 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8949 (mtm) REVERT: B 176 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8441 (mtp) REVERT: B 314 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 354 GLN cc_start: 0.8667 (pp30) cc_final: 0.8125 (pp30) REVERT: C 325 MET cc_start: 0.8756 (mmp) cc_final: 0.8487 (mmp) REVERT: C 354 GLN cc_start: 0.8929 (mp10) cc_final: 0.8613 (mp10) REVERT: D 354 GLN cc_start: 0.8499 (pp30) cc_final: 0.8180 (pp30) outliers start: 31 outliers final: 8 residues processed: 113 average time/residue: 1.8099 time to fit residues: 221.0606 Evaluate side-chains 102 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14960 Z= 0.266 Angle : 0.542 7.534 20310 Z= 0.249 Chirality : 0.044 0.132 2250 Planarity : 0.004 0.070 2600 Dihedral : 7.258 97.803 2087 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1835 helix: 0.79 (0.20), residues: 740 sheet: 1.08 (0.29), residues: 320 loop : 0.52 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE E 255 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.737 Fit side-chains REVERT: A 314 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: A 354 GLN cc_start: 0.8759 (pp30) cc_final: 0.8495 (pp30) REVERT: A 355 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9032 (mtp) REVERT: B 176 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8439 (mtp) REVERT: B 314 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: B 354 GLN cc_start: 0.8629 (pp30) cc_final: 0.8081 (pp30) REVERT: C 6 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8901 (p) REVERT: C 246 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: C 325 MET cc_start: 0.8842 (mmp) cc_final: 0.8515 (mmp) REVERT: C 354 GLN cc_start: 0.8958 (mp10) cc_final: 0.8626 (mp10) outliers start: 34 outliers final: 14 residues processed: 115 average time/residue: 1.6812 time to fit residues: 209.6606 Evaluate side-chains 110 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 chunk 152 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14960 Z= 0.211 Angle : 0.528 8.179 20310 Z= 0.240 Chirality : 0.043 0.131 2250 Planarity : 0.003 0.061 2600 Dihedral : 7.136 95.659 2087 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.17 % Allowed : 15.54 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1835 helix: 1.00 (0.20), residues: 740 sheet: 1.04 (0.30), residues: 315 loop : 0.55 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE E 255 TYR 0.005 0.001 TYR E 69 ARG 0.001 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.767 Fit side-chains REVERT: A 314 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: A 354 GLN cc_start: 0.8744 (pp30) cc_final: 0.8470 (pp30) REVERT: A 355 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9035 (mtp) REVERT: B 176 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8453 (mtp) REVERT: B 314 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: B 354 GLN cc_start: 0.8613 (pp30) cc_final: 0.8096 (pp30) REVERT: C 6 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 246 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: C 325 MET cc_start: 0.8836 (mmp) cc_final: 0.8495 (mmp) REVERT: C 354 GLN cc_start: 0.8957 (mp10) cc_final: 0.8610 (mp10) REVERT: E 6 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8711 (t) REVERT: E 355 MET cc_start: 0.9208 (mtp) cc_final: 0.8817 (mtm) outliers start: 34 outliers final: 14 residues processed: 116 average time/residue: 1.6463 time to fit residues: 207.3670 Evaluate side-chains 111 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN B 12 ASN B 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14960 Z= 0.344 Angle : 0.571 7.811 20310 Z= 0.264 Chirality : 0.045 0.138 2250 Planarity : 0.003 0.051 2600 Dihedral : 7.260 98.393 2087 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.55 % Allowed : 14.65 % Favored : 82.80 % 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: 1.17 (0.21), residues: 1835 helix: 1.05 (0.21), residues: 740 sheet: 1.12 (0.30), residues: 320 loop : 0.53 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE A 127 TYR 0.007 0.001 TYR A 188 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 91 time to evaluate : 1.812 Fit side-chains REVERT: A 314 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 354 GLN cc_start: 0.8787 (pp30) cc_final: 0.8454 (pp30) REVERT: A 355 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9017 (mtp) REVERT: B 176 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: B 314 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: B 354 GLN cc_start: 0.8624 (pp30) cc_final: 0.8127 (pp30) REVERT: C 6 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 51 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8650 (p0) REVERT: C 246 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: C 325 MET cc_start: 0.8909 (mmp) cc_final: 0.8663 (mmp) REVERT: C 354 GLN cc_start: 0.8954 (mp10) cc_final: 0.8604 (mp10) REVERT: E 6 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8708 (t) REVERT: E 99 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8773 (pm20) outliers start: 40 outliers final: 19 residues processed: 121 average time/residue: 1.6198 time to fit residues: 213.0091 Evaluate side-chains 117 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14960 Z= 0.146 Angle : 0.518 8.404 20310 Z= 0.233 Chirality : 0.043 0.135 2250 Planarity : 0.003 0.051 2600 Dihedral : 7.034 94.460 2087 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.46 % Allowed : 15.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1835 helix: 1.18 (0.20), residues: 740 sheet: 1.10 (0.31), residues: 315 loop : 0.59 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.000 HIS A 40 PHE 0.009 0.001 PHE E 255 TYR 0.006 0.000 TYR E 69 ARG 0.001 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.785 Fit side-chains REVERT: A 314 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: A 354 GLN cc_start: 0.8739 (pp30) cc_final: 0.8404 (pp30) REVERT: A 355 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.9007 (mtp) REVERT: B 314 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 354 GLN cc_start: 0.8608 (pp30) cc_final: 0.8116 (pp30) REVERT: C 246 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: C 325 MET cc_start: 0.8881 (mmp) cc_final: 0.8608 (mmp) REVERT: C 354 GLN cc_start: 0.8954 (mp10) cc_final: 0.8596 (mp10) REVERT: D 246 GLN cc_start: 0.8753 (mt0) cc_final: 0.8492 (mt0) REVERT: D 314 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8194 (tp40) REVERT: E 355 MET cc_start: 0.9228 (mtp) cc_final: 0.8814 (mtm) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 1.7461 time to fit residues: 204.4413 Evaluate side-chains 105 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14960 Z= 0.192 Angle : 0.528 8.797 20310 Z= 0.238 Chirality : 0.043 0.131 2250 Planarity : 0.003 0.045 2600 Dihedral : 7.005 94.203 2087 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.59 % Allowed : 16.05 % Favored : 82.36 % 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: 1.34 (0.21), residues: 1835 helix: 1.25 (0.21), residues: 740 sheet: 1.14 (0.31), residues: 315 loop : 0.60 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.000 HIS E 161 PHE 0.008 0.001 PHE E 255 TYR 0.006 0.000 TYR B 188 ARG 0.001 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.842 Fit side-chains REVERT: A 44 MET cc_start: 0.9230 (mmm) cc_final: 0.6761 (pmt) REVERT: A 314 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 354 GLN cc_start: 0.8741 (pp30) cc_final: 0.8411 (pp30) REVERT: A 355 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9003 (mtp) REVERT: B 314 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 354 GLN cc_start: 0.8595 (pp30) cc_final: 0.8078 (pp30) REVERT: C 6 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8941 (p) REVERT: C 246 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: C 325 MET cc_start: 0.8885 (mmp) cc_final: 0.8589 (mmp) REVERT: C 354 GLN cc_start: 0.8959 (mp10) cc_final: 0.8596 (mp10) REVERT: D 246 GLN cc_start: 0.8740 (mt0) cc_final: 0.8475 (mt0) REVERT: E 355 MET cc_start: 0.9218 (mtp) cc_final: 0.8828 (mtm) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 1.6455 time to fit residues: 198.2009 Evaluate side-chains 110 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 128 ASN C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14960 Z= 0.268 Angle : 0.554 8.962 20310 Z= 0.252 Chirality : 0.044 0.131 2250 Planarity : 0.003 0.045 2600 Dihedral : 7.095 96.046 2087 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.78 % Allowed : 15.67 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1835 helix: 1.24 (0.21), residues: 740 sheet: 1.10 (0.31), residues: 315 loop : 0.57 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 79 HIS 0.003 0.001 HIS E 161 PHE 0.008 0.001 PHE E 127 TYR 0.008 0.001 TYR B 188 ARG 0.001 0.000 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.818 Fit side-chains REVERT: A 314 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: A 354 GLN cc_start: 0.8749 (pp30) cc_final: 0.8389 (pp30) REVERT: A 355 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9007 (mtp) REVERT: B 314 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 354 GLN cc_start: 0.8591 (pp30) cc_final: 0.8075 (pp30) REVERT: C 6 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8944 (p) REVERT: C 325 MET cc_start: 0.8902 (mmp) cc_final: 0.8591 (mmp) REVERT: C 354 GLN cc_start: 0.8959 (mp10) cc_final: 0.8599 (mp10) REVERT: E 99 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: E 355 MET cc_start: 0.9207 (mtp) cc_final: 0.8928 (mtm) outliers start: 28 outliers final: 14 residues processed: 112 average time/residue: 1.6334 time to fit residues: 198.7552 Evaluate side-chains 110 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 0.0070 chunk 89 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 162 ASN B 41 GLN C 12 ASN C 246 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14960 Z= 0.126 Angle : 0.514 8.752 20310 Z= 0.230 Chirality : 0.042 0.134 2250 Planarity : 0.003 0.045 2600 Dihedral : 6.869 91.960 2087 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.21 % Allowed : 16.05 % Favored : 82.74 % 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: 1.40 (0.21), residues: 1835 helix: 1.29 (0.20), residues: 740 sheet: 1.17 (0.31), residues: 315 loop : 0.66 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.002 0.000 HIS E 161 PHE 0.008 0.001 PHE E 255 TYR 0.007 0.000 TYR B 69 ARG 0.001 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 2.069 Fit side-chains REVERT: A 44 MET cc_start: 0.9248 (mmm) cc_final: 0.6724 (pmt) REVERT: A 354 GLN cc_start: 0.8699 (pp30) cc_final: 0.8390 (pp30) REVERT: A 355 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9005 (mtp) REVERT: B 314 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: B 354 GLN cc_start: 0.8541 (pp30) cc_final: 0.8048 (pp30) REVERT: C 6 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8965 (p) REVERT: C 325 MET cc_start: 0.8892 (mmp) cc_final: 0.8581 (mmp) REVERT: C 354 GLN cc_start: 0.8958 (mp10) cc_final: 0.8579 (mp10) REVERT: D 246 GLN cc_start: 0.8737 (mt0) cc_final: 0.8425 (mt0) REVERT: E 355 MET cc_start: 0.9200 (mtp) cc_final: 0.8826 (mtm) outliers start: 19 outliers final: 11 residues processed: 110 average time/residue: 1.7808 time to fit residues: 213.6267 Evaluate side-chains 106 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.049154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.039277 restraints weight = 42119.043| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 2.88 r_work: 0.2430 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14960 Z= 0.117 Angle : 0.507 8.721 20310 Z= 0.225 Chirality : 0.042 0.132 2250 Planarity : 0.003 0.044 2600 Dihedral : 6.705 89.825 2087 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.83 % Allowed : 16.82 % Favored : 82.36 % 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: 1.45 (0.21), residues: 1835 helix: 1.42 (0.21), residues: 740 sheet: 0.92 (0.30), residues: 340 loop : 0.71 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.002 0.000 HIS A 40 PHE 0.007 0.001 PHE B 255 TYR 0.005 0.000 TYR E 69 ARG 0.001 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.14 seconds wall clock time: 77 minutes 22.06 seconds (4642.06 seconds total)