Starting phenix.real_space_refine (version: dev) on Mon Dec 12 19:25:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/12_2022/6kln_0712_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 7.14, per 1000 atoms: 0.61 Number of scatterers: 11748 At special positions: 0 Unit cell: (92.02, 96.3, 165.85, 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: 4.82 Conformation dependent library (CDL) restraints added in 1.9 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: 80 helices and 16 sheets defined 37.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 79 through 90 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 removed outlier: 3.757A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.759A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (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 192 removed outlier: 3.537A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.910A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.987A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 264 through 267 removed outlier: 3.615A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 267' Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.719A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.633A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) No H-bonds generated for '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 317 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.962A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 79 through 90 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 removed outlier: 3.757A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.758A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (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 192 removed outlier: 3.537A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.910A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.988A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.615A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.719A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.633A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 294' 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 317 Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.961A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' 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 removed outlier: 3.757A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.759A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (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 192 removed outlier: 3.537A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.910A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.987A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.616A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.718A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.633A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) No H-bonds generated for '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 317 Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.961A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' 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 removed outlier: 3.757A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.758A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (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 192 removed outlier: 3.536A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) 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 removed outlier: 3.909A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.988A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 removed outlier: 3.616A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.719A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.633A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) No H-bonds generated for '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 317 Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.961A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.476A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.908A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (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: 6.476A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.907A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (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: 6.476A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.907A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (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: 6.476A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.907A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 296 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 5.16 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: 3840 1.34 - 1.46: 2624 1.46 - 1.58: 5380 1.58 - 1.70: 12 1.70 - 1.82: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" CG HIC D 73 " pdb=" CD2 HIC D 73 " ideal model delta sigma weight residual 1.369 1.407 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.13: 370 106.13 - 113.43: 6688 113.43 - 120.72: 5471 120.72 - 128.01: 3644 128.01 - 135.31: 119 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N ILE A 267 " pdb=" CA ILE A 267 " pdb=" C ILE A 267 " ideal model delta sigma weight residual 111.91 108.86 3.05 8.90e-01 1.26e+00 1.18e+01 angle pdb=" N ILE C 267 " pdb=" CA ILE C 267 " pdb=" C ILE C 267 " ideal model delta sigma weight residual 111.91 108.89 3.02 8.90e-01 1.26e+00 1.15e+01 angle pdb=" N ILE B 267 " pdb=" CA ILE B 267 " pdb=" C ILE B 267 " ideal model delta sigma weight residual 111.91 108.91 3.00 8.90e-01 1.26e+00 1.14e+01 angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 111.91 108.92 2.99 8.90e-01 1.26e+00 1.13e+01 angle pdb=" C ALA C 22 " pdb=" N GLY C 23 " pdb=" CA GLY C 23 " ideal model delta sigma weight residual 123.30 120.24 3.06 1.06e+00 8.90e-01 8.34e+00 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6296 17.74 - 35.48: 736 35.48 - 53.21: 128 53.21 - 70.95: 48 70.95 - 88.69: 12 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" CA SER D 232 " pdb=" C SER D 232 " pdb=" N SER D 233 " pdb=" CA SER D 233 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER A 232 " pdb=" C SER A 232 " pdb=" N SER A 233 " pdb=" CA SER A 233 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER C 232 " pdb=" C SER C 232 " pdb=" N SER C 233 " pdb=" CA SER C 233 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 853 0.035 - 0.070: 612 0.070 - 0.105: 246 0.105 - 0.140: 93 0.140 - 0.175: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB VAL D 152 " pdb=" CA VAL D 152 " pdb=" CG1 VAL D 152 " pdb=" CG2 VAL D 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 152 " pdb=" CA VAL B 152 " pdb=" CG1 VAL B 152 " pdb=" CG2 VAL B 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CB VAL A 152 " pdb=" CA VAL A 152 " pdb=" CG1 VAL A 152 " pdb=" CG2 VAL A 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" C GLU B 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU B 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLU A 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU A 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 8542 3.10 - 3.70: 17180 3.70 - 4.30: 25674 4.30 - 4.90: 43699 Nonbonded interactions: 95206 Sorted by model distance: nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 1.904 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 1.904 2.170 nonbonded pdb=" O SER A 33 " pdb=" OG SER A 33 " model vdw 2.168 2.440 ... (remaining 95201 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 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. 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: 1.610 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: 4.940 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.130 Process input model: 34.380 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 Set scattering table: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.009 0.058 12004 Z= 0.618 Angle : 0.859 8.181 16292 Z= 0.486 Chirality : 0.053 0.175 1808 Planarity : 0.004 0.038 2084 Dihedral : 16.338 88.687 4468 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 11.46 % 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: -4.65 (0.17), residues: 1468 helix: -3.50 (0.15), residues: 580 sheet: -2.92 (0.28), residues: 220 loop : -2.59 (0.19), residues: 668 *********************** 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 224 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 80 time to evaluate : 1.542 Fit side-chains outliers start: 144 outliers final: 34 residues processed: 217 average time/residue: 0.1996 time to fit residues: 65.8339 Evaluate side-chains 101 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 67 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1031 time to fit residues: 9.0163 ------------------------------------------------------------------------------- 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: 10.0000 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 161 HIS A 162 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 161 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 161 HIS C 162 ASN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 161 HIS D 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12004 Z= 0.166 Angle : 0.571 5.809 16292 Z= 0.279 Chirality : 0.044 0.145 1808 Planarity : 0.003 0.033 2084 Dihedral : 7.048 68.085 1672 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.27 % 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: -3.17 (0.19), residues: 1468 helix: -2.33 (0.18), residues: 588 sheet: -2.02 (0.29), residues: 228 loop : -1.73 (0.22), residues: 652 *********************** 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 85 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.575 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 80 average time/residue: 0.2010 time to fit residues: 25.8907 Evaluate side-chains 71 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1011 time to fit residues: 3.1237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 12004 Z= 0.473 Angle : 0.703 6.900 16292 Z= 0.344 Chirality : 0.047 0.155 1808 Planarity : 0.004 0.031 2084 Dihedral : 7.168 69.733 1672 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 1.19 % 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: -2.38 (0.20), residues: 1468 helix: -1.71 (0.20), residues: 588 sheet: -1.47 (0.32), residues: 236 loop : -1.28 (0.23), residues: 644 *********************** 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 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.373 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.2207 time to fit residues: 26.2573 Evaluate side-chains 72 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1046 time to fit residues: 3.0894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 0.0270 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 354 GLN C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12004 Z= 0.162 Angle : 0.538 5.968 16292 Z= 0.254 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.526 61.518 1672 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.48 % 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: -1.73 (0.21), residues: 1468 helix: -1.26 (0.21), residues: 588 sheet: -1.23 (0.33), residues: 236 loop : -0.78 (0.24), residues: 644 *********************** 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 74 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.585 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 72 average time/residue: 0.2270 time to fit residues: 25.6096 Evaluate side-chains 68 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1333 time to fit residues: 2.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 12004 Z= 0.351 Angle : 0.606 5.998 16292 Z= 0.291 Chirality : 0.045 0.143 1808 Planarity : 0.004 0.029 2084 Dihedral : 6.622 61.037 1672 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.56 % 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: -1.32 (0.22), residues: 1468 helix: -0.86 (0.21), residues: 588 sheet: -1.01 (0.34), residues: 244 loop : -0.61 (0.25), residues: 636 *********************** 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 74 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.499 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.2181 time to fit residues: 25.2355 Evaluate side-chains 72 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1159 time to fit residues: 3.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 overall best weight: 4.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12004 Z= 0.289 Angle : 0.576 5.971 16292 Z= 0.273 Chirality : 0.045 0.133 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.507 61.104 1672 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.64 % 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: -1.01 (0.22), residues: 1468 helix: -0.58 (0.22), residues: 588 sheet: -0.89 (0.35), residues: 244 loop : -0.44 (0.25), residues: 636 *********************** 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 74 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.386 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.2019 time to fit residues: 23.4911 Evaluate side-chains 71 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1134 time to fit residues: 2.9850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12004 Z= 0.240 Angle : 0.552 5.923 16292 Z= 0.261 Chirality : 0.044 0.152 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.316 60.822 1672 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.16 % 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: -0.73 (0.22), residues: 1468 helix: -0.36 (0.22), residues: 592 sheet: -0.80 (0.35), residues: 244 loop : -0.24 (0.25), residues: 632 *********************** 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 70 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.516 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.2256 time to fit residues: 24.3421 Evaluate side-chains 69 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1179 time to fit residues: 2.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 12004 Z= 0.299 Angle : 0.588 10.545 16292 Z= 0.279 Chirality : 0.044 0.136 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.365 60.973 1672 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.32 % 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: -0.66 (0.23), residues: 1468 helix: -0.29 (0.22), residues: 592 sheet: -0.80 (0.35), residues: 244 loop : -0.19 (0.25), residues: 632 *********************** 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 71 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.593 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 0.2116 time to fit residues: 23.0975 Evaluate side-chains 67 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1401 time to fit residues: 2.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3591 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= 0.174 Angle : 0.543 9.575 16292 Z= 0.252 Chirality : 0.043 0.135 1808 Planarity : 0.003 0.026 2084 Dihedral : 6.044 60.594 1672 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.24 % 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: -0.51 (0.23), residues: 1468 helix: -0.21 (0.22), residues: 596 sheet: -0.74 (0.35), residues: 244 loop : -0.06 (0.25), residues: 628 *********************** 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 69 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.368 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 0.2002 time to fit residues: 21.9101 Evaluate side-chains 66 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 97 optimal weight: 10.0000 chunk 147 optimal weight: 0.0370 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12004 Z= 0.191 Angle : 0.540 6.774 16292 Z= 0.254 Chirality : 0.043 0.148 1808 Planarity : 0.003 0.026 2084 Dihedral : 5.925 59.935 1672 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.24 % 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 (0.23), residues: 1468 helix: -0.15 (0.22), residues: 596 sheet: -0.70 (0.35), residues: 244 loop : -0.02 (0.25), residues: 628 ********************** 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 68 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.481 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.2028 time to fit residues: 22.0106 Evaluate side-chains 65 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.028408 restraints weight = 76169.409| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 4.03 r_work: 0.2495 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12004 Z= 0.244 Angle : 0.561 8.355 16292 Z= 0.262 Chirality : 0.044 0.146 1808 Planarity : 0.003 0.026 2084 Dihedral : 5.967 59.765 1672 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.16 % 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: -0.09 (0.22), residues: 596 sheet: -0.70 (0.35), residues: 244 loop : -0.01 (0.25), residues: 628 =============================================================================== Job complete usr+sys time: 1787.77 seconds wall clock time: 33 minutes 53.37 seconds (2033.37 seconds total)