Starting phenix.real_space_refine on Thu Feb 15 09:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmx_27548/02_2024/8dmx_27548_updated.pdb" } resolution = 3.37 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 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} Time building chain proxies: 6.64, per 1000 atoms: 0.57 Number of scatterers: 11748 At special positions: 0 Unit cell: (79.299, 105.138, 170.181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 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: 4.46 Conformation dependent library (CDL) restraints added in 2.2 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 16 sheets defined 40.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 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 81 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 126 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.692A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.559A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.567A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.530A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.513A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.768A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) 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 81 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 126 Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.692A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) 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 195 removed outlier: 3.559A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.567A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.530A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.513A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.768A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (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 81 through 91 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 126 Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.692A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.558A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.568A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.530A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 339 through 348 removed outlier: 3.513A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.769A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (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 81 through 91 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 126 Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.692A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.559A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.567A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.530A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.513A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.767A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.912A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.624A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.719A pdb=" N ILE A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (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: 6.912A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.477A 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 removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.719A pdb=" N ILE B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (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: 6.911A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.477A 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 removed outlier: 3.624A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.719A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (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: 6.911A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.476A 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 removed outlier: 3.624A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.720A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 160 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 355 hydrogen bonds defined for protein. 921 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: 3.28 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3824 1.34 - 1.46: 2391 1.46 - 1.58: 5629 1.58 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.84e+00 bond pdb=" N ILE B 71 " pdb=" CA ILE B 71 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.85e+00 bond pdb=" N ILE A 71 " pdb=" CA ILE A 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.79e+00 bond pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.63: 440 106.63 - 113.98: 6837 113.98 - 121.33: 5921 121.33 - 128.69: 3014 128.69 - 136.04: 80 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CA ASN A 12 " pdb=" C ASN A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 115.51 120.24 -4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" CA ASN D 296 " pdb=" C ASN D 296 " pdb=" O ASN D 296 " ideal model delta sigma weight residual 121.20 117.51 3.69 1.04e+00 9.25e-01 1.26e+01 angle pdb=" CA ASN A 296 " pdb=" C ASN A 296 " pdb=" O ASN A 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN B 296 " pdb=" C ASN B 296 " pdb=" O ASN B 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN C 296 " pdb=" C ASN C 296 " pdb=" O ASN C 296 " ideal model delta sigma weight residual 121.20 117.56 3.64 1.04e+00 9.25e-01 1.22e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 6744 21.12 - 42.25: 404 42.25 - 63.37: 52 63.37 - 84.49: 12 84.49 - 105.62: 8 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 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 -60.00 -165.62 105.62 1 2.00e+01 2.50e-03 3.05e+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 -165.61 105.61 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -165.60 105.59 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1127 0.032 - 0.065: 447 0.065 - 0.097: 136 0.097 - 0.130: 86 0.130 - 0.162: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 12 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ASN A 12 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 12 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 13 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO D 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO B 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO B 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE B 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 10325 3.22 - 3.78: 16163 3.78 - 4.34: 22965 4.34 - 4.90: 38498 Nonbonded interactions: 88072 Sorted by model distance: nonbonded pdb="MG MG D 400 " pdb=" O1B ADP D 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG B 400 " pdb=" O1B ADP B 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG A 400 " pdb=" O1B ADP A 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG C 400 " pdb=" O1B ADP C 401 " model vdw 2.106 2.170 nonbonded pdb=" O ASP C 51 " pdb=" OD1 ASP C 51 " model vdw 2.144 3.040 ... (remaining 88067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.450 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.090 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.003 0.036 12004 Z= 0.184 Angle : 0.585 5.718 16292 Z= 0.328 Chirality : 0.044 0.162 1808 Planarity : 0.005 0.052 2084 Dihedral : 13.993 105.617 4468 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 0.17 (0.23), residues: 1468 helix: 1.05 (0.24), residues: 524 sheet: -0.19 (0.32), residues: 276 loop : -0.42 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 356 HIS 0.002 0.000 HIS C 101 PHE 0.009 0.001 PHE B 124 TYR 0.009 0.001 TYR A 294 ARG 0.013 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.440 Fit side-chains REVERT: A 326 LYS cc_start: 0.8167 (pttt) cc_final: 0.7755 (mttm) REVERT: B 47 MET cc_start: 0.4355 (ptm) cc_final: 0.4129 (ptp) REVERT: B 143 TYR cc_start: 0.7885 (m-10) cc_final: 0.7299 (m-80) REVERT: B 184 ASP cc_start: 0.8015 (m-30) cc_final: 0.7745 (m-30) REVERT: C 364 GLU cc_start: 0.8651 (tt0) cc_final: 0.8412 (tm-30) REVERT: D 47 MET cc_start: 0.3966 (ptm) cc_final: 0.3710 (ppp) REVERT: D 91 TYR cc_start: 0.7417 (m-80) cc_final: 0.6901 (m-80) REVERT: D 123 MET cc_start: 0.6921 (tpp) cc_final: 0.6677 (tpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2384 time to fit residues: 72.8126 Evaluate side-chains 129 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 275 HIS B 12 ASN B 275 HIS D 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 12004 Z= 0.524 Angle : 0.757 12.271 16292 Z= 0.380 Chirality : 0.053 0.181 1808 Planarity : 0.006 0.049 2084 Dihedral : 6.267 72.859 1672 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.47 % Allowed : 9.87 % Favored : 87.66 % 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: -0.72 (0.22), residues: 1468 helix: 0.31 (0.23), residues: 512 sheet: -0.50 (0.32), residues: 264 loop : -0.99 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 340 HIS 0.007 0.002 HIS D 161 PHE 0.017 0.002 PHE C 255 TYR 0.015 0.002 TYR B 218 ARG 0.007 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.334 Fit side-chains REVERT: A 326 LYS cc_start: 0.8372 (pttt) cc_final: 0.8018 (ptpp) REVERT: C 157 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8219 (t0) REVERT: D 47 MET cc_start: 0.3671 (ptm) cc_final: 0.3314 (ppp) REVERT: D 355 MET cc_start: 0.8795 (mtt) cc_final: 0.8565 (mtp) outliers start: 31 outliers final: 23 residues processed: 130 average time/residue: 0.2133 time to fit residues: 41.2689 Evaluate side-chains 112 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12004 Z= 0.260 Angle : 0.569 6.461 16292 Z= 0.279 Chirality : 0.046 0.138 1808 Planarity : 0.005 0.051 2084 Dihedral : 5.788 58.365 1672 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 13.14 % Favored : 84.55 % 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: -0.69 (0.22), residues: 1468 helix: 0.18 (0.23), residues: 536 sheet: -0.55 (0.32), residues: 264 loop : -0.84 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 356 HIS 0.004 0.001 HIS D 161 PHE 0.012 0.001 PHE C 255 TYR 0.010 0.001 TYR D 69 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.183 Fit side-chains REVERT: A 326 LYS cc_start: 0.8378 (pttt) cc_final: 0.7918 (ptpp) REVERT: D 47 MET cc_start: 0.3643 (ptm) cc_final: 0.3360 (ppp) REVERT: D 355 MET cc_start: 0.8770 (mtt) cc_final: 0.8541 (mtp) outliers start: 29 outliers final: 22 residues processed: 114 average time/residue: 0.1993 time to fit residues: 35.2267 Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12004 Z= 0.158 Angle : 0.507 6.327 16292 Z= 0.243 Chirality : 0.043 0.136 1808 Planarity : 0.004 0.050 2084 Dihedral : 5.367 56.867 1672 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.23 % Allowed : 13.46 % Favored : 84.32 % 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: -0.44 (0.22), residues: 1468 helix: 0.38 (0.24), residues: 540 sheet: -0.55 (0.33), residues: 232 loop : -0.63 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.002 0.001 HIS D 101 PHE 0.011 0.001 PHE A 31 TYR 0.008 0.001 TYR D 69 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.357 Fit side-chains REVERT: A 194 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (p) REVERT: A 326 LYS cc_start: 0.8382 (pttt) cc_final: 0.7888 (ptpp) REVERT: D 47 MET cc_start: 0.3643 (ptm) cc_final: 0.3404 (ppp) REVERT: D 176 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7562 (mtt) REVERT: D 355 MET cc_start: 0.8748 (mtt) cc_final: 0.8528 (mtp) outliers start: 28 outliers final: 17 residues processed: 118 average time/residue: 0.2226 time to fit residues: 39.1918 Evaluate side-chains 112 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 2 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12004 Z= 0.235 Angle : 0.541 6.029 16292 Z= 0.262 Chirality : 0.045 0.158 1808 Planarity : 0.005 0.052 2084 Dihedral : 5.362 61.776 1672 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.31 % Allowed : 14.09 % Favored : 83.60 % 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: -0.63 (0.22), residues: 1468 helix: 0.12 (0.23), residues: 564 sheet: -0.62 (0.33), residues: 232 loop : -0.68 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS D 161 PHE 0.012 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.365 Fit side-chains REVERT: A 261 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 326 LYS cc_start: 0.8362 (pttt) cc_final: 0.7837 (ptpp) REVERT: D 25 ASP cc_start: 0.8231 (p0) cc_final: 0.7861 (m-30) REVERT: D 355 MET cc_start: 0.8731 (mtt) cc_final: 0.8504 (mtp) outliers start: 29 outliers final: 22 residues processed: 116 average time/residue: 0.2091 time to fit residues: 37.1757 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.0670 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 0.0370 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 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 B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12004 Z= 0.126 Angle : 0.500 9.450 16292 Z= 0.237 Chirality : 0.043 0.162 1808 Planarity : 0.004 0.050 2084 Dihedral : 5.091 57.030 1672 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.15 % Allowed : 14.81 % Favored : 83.04 % 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: -0.43 (0.22), residues: 1468 helix: 0.27 (0.23), residues: 564 sheet: -0.53 (0.33), residues: 232 loop : -0.54 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.002 0.001 HIS D 101 PHE 0.011 0.001 PHE D 31 TYR 0.007 0.001 TYR B 69 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 1.522 Fit side-chains REVERT: A 261 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 326 LYS cc_start: 0.8371 (pttt) cc_final: 0.7817 (ptpp) REVERT: D 25 ASP cc_start: 0.8211 (p0) cc_final: 0.7860 (m-30) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.2073 time to fit residues: 37.5023 Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12004 Z= 0.257 Angle : 0.556 6.610 16292 Z= 0.270 Chirality : 0.046 0.158 1808 Planarity : 0.005 0.056 2084 Dihedral : 5.281 61.899 1672 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.47 % Allowed : 14.25 % Favored : 83.28 % 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: -0.55 (0.22), residues: 1468 helix: 0.14 (0.23), residues: 560 sheet: -0.52 (0.31), residues: 264 loop : -0.60 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR B 218 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.402 Fit side-chains REVERT: A 261 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7625 (mp) REVERT: A 326 LYS cc_start: 0.8403 (pttt) cc_final: 0.7829 (ptpp) REVERT: C 157 ASP cc_start: 0.8339 (t0) cc_final: 0.8099 (t0) REVERT: D 25 ASP cc_start: 0.8242 (p0) cc_final: 0.7903 (m-30) outliers start: 31 outliers final: 24 residues processed: 116 average time/residue: 0.2256 time to fit residues: 39.8943 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12004 Z= 0.143 Angle : 0.502 6.571 16292 Z= 0.239 Chirality : 0.043 0.169 1808 Planarity : 0.004 0.049 2084 Dihedral : 5.024 57.659 1672 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.99 % Allowed : 14.89 % Favored : 83.12 % 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: -0.39 (0.23), residues: 1468 helix: 0.26 (0.23), residues: 564 sheet: -0.51 (0.33), residues: 236 loop : -0.48 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.002 0.001 HIS C 101 PHE 0.011 0.001 PHE D 31 TYR 0.007 0.001 TYR D 69 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.457 Fit side-chains REVERT: A 326 LYS cc_start: 0.8344 (pttt) cc_final: 0.7773 (ptpp) REVERT: C 246 GLN cc_start: 0.7649 (mt0) cc_final: 0.7342 (mt0) REVERT: D 25 ASP cc_start: 0.8224 (p0) cc_final: 0.7901 (m-30) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.2431 time to fit residues: 42.6622 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 0.0010 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12004 Z= 0.169 Angle : 0.512 7.041 16292 Z= 0.244 Chirality : 0.044 0.168 1808 Planarity : 0.004 0.053 2084 Dihedral : 4.966 57.542 1672 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 14.89 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1468 helix: 0.50 (0.24), residues: 544 sheet: -0.48 (0.33), residues: 236 loop : -0.55 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 356 HIS 0.002 0.001 HIS D 101 PHE 0.011 0.001 PHE D 31 TYR 0.007 0.001 TYR D 69 ARG 0.007 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.424 Fit side-chains REVERT: A 261 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 326 LYS cc_start: 0.8336 (pttt) cc_final: 0.7766 (ptpp) REVERT: B 194 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7308 (p) REVERT: C 246 GLN cc_start: 0.7672 (mt0) cc_final: 0.7377 (mt0) REVERT: D 25 ASP cc_start: 0.8244 (p0) cc_final: 0.7932 (m-30) outliers start: 24 outliers final: 21 residues processed: 113 average time/residue: 0.2182 time to fit residues: 37.2627 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12004 Z= 0.254 Angle : 0.550 6.724 16292 Z= 0.267 Chirality : 0.046 0.166 1808 Planarity : 0.004 0.052 2084 Dihedral : 5.185 62.705 1672 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.99 % Allowed : 15.13 % Favored : 82.88 % 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: -0.54 (0.22), residues: 1468 helix: 0.15 (0.23), residues: 560 sheet: -0.49 (0.30), residues: 268 loop : -0.62 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.012 0.001 PHE D 31 TYR 0.008 0.001 TYR B 218 ARG 0.008 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.430 Fit side-chains REVERT: A 261 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 326 LYS cc_start: 0.8336 (pttt) cc_final: 0.7736 (ptpp) REVERT: B 194 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7316 (p) REVERT: D 25 ASP cc_start: 0.8250 (p0) cc_final: 0.7943 (m-30) outliers start: 25 outliers final: 21 residues processed: 112 average time/residue: 0.2043 time to fit residues: 35.1980 Evaluate side-chains 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 0.0020 chunk 14 optimal weight: 0.0070 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087360 restraints weight = 17376.859| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.24 r_work: 0.2859 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12004 Z= 0.144 Angle : 0.500 6.400 16292 Z= 0.238 Chirality : 0.043 0.174 1808 Planarity : 0.004 0.050 2084 Dihedral : 4.929 56.525 1672 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.83 % Allowed : 15.21 % Favored : 82.96 % 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: -0.42 (0.22), residues: 1468 helix: 0.24 (0.23), residues: 568 sheet: -0.49 (0.33), residues: 236 loop : -0.53 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS D 101 PHE 0.012 0.001 PHE D 31 TYR 0.006 0.001 TYR D 69 ARG 0.008 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.71 seconds wall clock time: 44 minutes 0.66 seconds (2640.66 seconds total)