Starting phenix.real_space_refine on Mon Apr 6 20:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9p_72712/04_2026/9y9p_72712_neut.cif" } resolution = 2.06 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 120 5.16 5 C 13315 2.51 5 N 3500 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21371 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} 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: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "c" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, b, c, d, e Time building chain proxies: 4.21, per 1000 atoms: 0.20 Number of scatterers: 21371 At special positions: 0 Unit cell: (100.44, 126.36, 206.82, 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 120 16.00 P 10 15.00 Mg 5 11.99 O 4421 8.00 N 3500 7.00 C 13315 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 - 3.00 Amino acid : True - 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: 1.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4980 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 35 sheets defined 48.3% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.679A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.703A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.573A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.843A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.726A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.349A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 356 removed outlier: 6.555A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.679A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.703A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.572A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.843A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.727A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.348A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 356 removed outlier: 6.555A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.679A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 61' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.704A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.571A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.843A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.726A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.349A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 356 removed outlier: 6.555A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.678A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 61' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.702A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.573A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.844A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.727A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.349A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 356 removed outlier: 6.556A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.678A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS E 61 " --> pdb=" O ALA E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.704A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.573A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.844A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.727A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.349A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 356 removed outlier: 6.556A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.740A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 73 Processing helix chain 'a' and resid 110 through 128 removed outlier: 5.210A pdb=" N ASP a 122 " --> pdb=" O ALA a 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 Processing helix chain 'a' and resid 145 through 153 removed outlier: 4.193A pdb=" N LEU a 149 " --> pdb=" O ASP a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 156 No H-bonds generated for 'chain 'a' and resid 154 through 156' Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.740A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 110 through 128 removed outlier: 5.210A pdb=" N ASP b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA b 123 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.193A pdb=" N LEU b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.740A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL c 20 " --> pdb=" O ASN c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 31 Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 73 Processing helix chain 'c' and resid 110 through 128 removed outlier: 5.212A pdb=" N ASP c 122 " --> pdb=" O ALA c 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 Processing helix chain 'c' and resid 145 through 153 removed outlier: 4.193A pdb=" N LEU c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 20 removed outlier: 3.740A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL d 20 " --> pdb=" O ASN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 31 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 73 Processing helix chain 'd' and resid 110 through 128 removed outlier: 5.211A pdb=" N ASP d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 Processing helix chain 'd' and resid 145 through 153 removed outlier: 4.193A pdb=" N LEU d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.740A pdb=" N ILE e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL e 20 " --> pdb=" O ASN e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 31 Processing helix chain 'e' and resid 58 through 60 No H-bonds generated for 'chain 'e' and resid 58 through 60' Processing helix chain 'e' and resid 66 through 73 Processing helix chain 'e' and resid 110 through 128 removed outlier: 5.211A pdb=" N ASP e 122 " --> pdb=" O ALA e 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA e 123 " --> pdb=" O SER e 119 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 Processing helix chain 'e' and resid 145 through 153 removed outlier: 4.194A pdb=" N LEU e 149 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 156 No H-bonds generated for 'chain 'e' and resid 154 through 156' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.923A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.387A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.925A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.387A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.924A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.387A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.925A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.387A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.925A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.386A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.284A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.284A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS e 133 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.283A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 2.44 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: 5834 1.34 - 1.45: 3637 1.45 - 1.57: 11754 1.57 - 1.69: 15 1.69 - 1.81: 205 Bond restraints: 21445 Sorted by residual: bond pdb=" CG LEU c 111 " pdb=" CD1 LEU c 111 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.12e+00 bond pdb=" CG LEU d 111 " pdb=" CD1 LEU d 111 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.07e+00 bond pdb=" CG LEU a 111 " pdb=" CD1 LEU a 111 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.05e+00 bond pdb=" CG LEU b 111 " pdb=" CD1 LEU b 111 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.01e+00 bond pdb=" CG LEU e 111 " pdb=" CD1 LEU e 111 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.97e+00 ... (remaining 21440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 27803 2.40 - 4.81: 1086 4.81 - 7.21: 115 7.21 - 9.62: 46 9.62 - 12.02: 10 Bond angle restraints: 29060 Sorted by residual: angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" CB GLU A 364 " ideal model delta sigma weight residual 110.20 118.37 -8.17 1.49e+00 4.50e-01 3.00e+01 angle pdb=" N GLU E 364 " pdb=" CA GLU E 364 " pdb=" CB GLU E 364 " ideal model delta sigma weight residual 110.20 118.35 -8.15 1.49e+00 4.50e-01 2.99e+01 angle pdb=" N GLU C 364 " pdb=" CA GLU C 364 " pdb=" CB GLU C 364 " ideal model delta sigma weight residual 110.20 118.34 -8.14 1.49e+00 4.50e-01 2.98e+01 angle pdb=" N GLU D 364 " pdb=" CA GLU D 364 " pdb=" CB GLU D 364 " ideal model delta sigma weight residual 110.20 118.34 -8.14 1.49e+00 4.50e-01 2.98e+01 angle pdb=" N GLU B 364 " pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " ideal model delta sigma weight residual 110.20 118.33 -8.13 1.49e+00 4.50e-01 2.98e+01 ... (remaining 29055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11974 17.30 - 34.60: 881 34.60 - 51.90: 140 51.90 - 69.19: 40 69.19 - 86.49: 40 Dihedral angle restraints: 13075 sinusoidal: 5325 harmonic: 7750 Sorted by residual: dihedral pdb=" C5' ADP E 400 " pdb=" O5' ADP E 400 " pdb=" PA ADP E 400 " pdb=" O2A ADP E 400 " ideal model delta sinusoidal sigma weight residual -60.00 26.50 -86.49 1 2.00e+01 2.50e-03 2.25e+01 dihedral pdb=" C5' ADP B 400 " pdb=" O5' ADP B 400 " pdb=" PA ADP B 400 " pdb=" O2A ADP B 400 " ideal model delta sinusoidal sigma weight residual -60.00 26.42 -86.41 1 2.00e+01 2.50e-03 2.25e+01 dihedral pdb=" C5' ADP C 400 " pdb=" O5' ADP C 400 " pdb=" PA ADP C 400 " pdb=" O2A ADP C 400 " ideal model delta sinusoidal sigma weight residual -60.00 26.37 -86.37 1 2.00e+01 2.50e-03 2.25e+01 ... (remaining 13072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2148 0.054 - 0.108: 904 0.108 - 0.162: 154 0.162 - 0.216: 44 0.216 - 0.270: 20 Chirality restraints: 3270 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3267 not shown) Planarity restraints: 3690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 370 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C VAL D 370 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL D 370 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS D 371 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 370 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL C 370 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL C 370 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS C 371 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 370 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C VAL A 370 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 370 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS A 371 " 0.020 2.00e-02 2.50e+03 ... (remaining 3687 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 50 2.63 - 3.20: 17781 3.20 - 3.77: 32872 3.77 - 4.33: 49868 4.33 - 4.90: 76821 Nonbonded interactions: 177392 Sorted by model distance: nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.067 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.067 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.067 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.067 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.067 2.170 ... (remaining 177387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 23.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.070 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.006 0.088 21445 Z= 0.309 Angle : 1.115 12.021 29060 Z= 0.613 Chirality : 0.062 0.270 3270 Planarity : 0.009 0.063 3690 Dihedral : 13.596 86.493 8095 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.15), residues: 2615 helix: -2.06 (0.13), residues: 1035 sheet: 0.13 (0.23), residues: 510 loop : -0.15 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 312 TYR 0.017 0.002 TYR C 91 PHE 0.048 0.004 PHE C 90 TRP 0.019 0.004 TRP A 86 HIS 0.010 0.002 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00626 (21445) covalent geometry : angle 1.11454 (29060) hydrogen bonds : bond 0.17289 ( 1015) hydrogen bonds : angle 7.04148 ( 2805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8695 (mttp) cc_final: 0.8360 (mmtm) REVERT: A 372 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7100 (mtm110) REVERT: B 68 LYS cc_start: 0.8643 (mttp) cc_final: 0.8271 (mmtm) REVERT: B 225 ASN cc_start: 0.7674 (t0) cc_final: 0.7459 (m110) REVERT: B 372 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7184 (mtm110) REVERT: C 68 LYS cc_start: 0.8599 (mttp) cc_final: 0.8215 (mmtm) REVERT: C 276 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 372 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7066 (mtm110) REVERT: D 68 LYS cc_start: 0.8555 (mttp) cc_final: 0.8196 (mmtm) REVERT: D 80 ASP cc_start: 0.7984 (m-30) cc_final: 0.7719 (m-30) REVERT: D 372 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7030 (mtm110) REVERT: E 68 LYS cc_start: 0.8552 (mttp) cc_final: 0.8235 (mmtm) REVERT: E 125 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7641 (mt-10) REVERT: E 276 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8618 (tt0) REVERT: a 78 ASN cc_start: 0.8424 (m-40) cc_final: 0.7768 (p0) REVERT: b 78 ASN cc_start: 0.8466 (m-40) cc_final: 0.7747 (p0) REVERT: b 164 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7491 (mttp) REVERT: c 146 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7706 (ptm160) REVERT: c 164 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7491 (mttp) REVERT: d 31 LYS cc_start: 0.7659 (mmpt) cc_final: 0.7340 (mppt) REVERT: d 146 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7722 (ptm160) REVERT: e 31 LYS cc_start: 0.7487 (mmpt) cc_final: 0.7199 (mppt) REVERT: e 112 LYS cc_start: 0.8580 (tttp) cc_final: 0.8360 (mtmm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.7859 time to fit residues: 351.6924 Evaluate side-chains 295 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 115 ASN A 173 HIS B A 246 GLN B 101 HIS B 115 ASN B 173 HIS B B 246 GLN C 101 HIS C 115 ASN C 173 HIS B D 101 HIS D 115 ASN D 121 GLN D 246 GLN E 101 HIS E 115 ASN E 121 GLN E 246 GLN a 16 ASN a 46 GLN b 16 ASN b 46 GLN c 46 GLN d 16 ASN e 16 ASN e 46 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111097 restraints weight = 63104.749| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.35 r_work: 0.2975 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21445 Z= 0.135 Angle : 0.649 7.442 29060 Z= 0.334 Chirality : 0.046 0.191 3270 Planarity : 0.005 0.044 3690 Dihedral : 6.654 86.796 2955 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.61 % Allowed : 5.19 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2615 helix: -0.29 (0.16), residues: 1025 sheet: 0.36 (0.23), residues: 560 loop : 0.82 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 210 TYR 0.012 0.001 TYR A 69 PHE 0.023 0.002 PHE C 90 TRP 0.015 0.002 TRP B 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00272 (21445) covalent geometry : angle 0.64902 (29060) hydrogen bonds : bond 0.05416 ( 1015) hydrogen bonds : angle 5.30193 ( 2805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 313 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8760 (mttp) cc_final: 0.8473 (mmtm) REVERT: B 68 LYS cc_start: 0.8886 (mttp) cc_final: 0.8591 (mmtm) REVERT: B 237 GLU cc_start: 0.8232 (tp30) cc_final: 0.8012 (mm-30) REVERT: B 372 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7478 (mtm110) REVERT: C 68 LYS cc_start: 0.8903 (mttp) cc_final: 0.8581 (mmtm) REVERT: D 68 LYS cc_start: 0.8868 (mttp) cc_final: 0.8546 (mmtm) REVERT: E 68 LYS cc_start: 0.8814 (mttp) cc_final: 0.8462 (mmtm) REVERT: E 125 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7822 (mt-10) REVERT: E 276 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8886 (tt0) REVERT: a 78 ASN cc_start: 0.8597 (m-40) cc_final: 0.7853 (p0) REVERT: b 78 ASN cc_start: 0.8672 (m-40) cc_final: 0.7913 (p0) REVERT: b 144 LYS cc_start: 0.8377 (tttm) cc_final: 0.8107 (ttpm) REVERT: c 92 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7742 (mtmm) REVERT: c 146 ARG cc_start: 0.8218 (ptm-80) cc_final: 0.7829 (ptm160) REVERT: d 31 LYS cc_start: 0.7510 (mmpt) cc_final: 0.6973 (mppt) REVERT: d 146 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7635 (ptm160) REVERT: e 31 LYS cc_start: 0.7150 (mmpt) cc_final: 0.6585 (mppt) REVERT: e 112 LYS cc_start: 0.8520 (tttp) cc_final: 0.8256 (ttpt) REVERT: e 126 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8136 (ptpp) outliers start: 14 outliers final: 2 residues processed: 319 average time/residue: 0.7434 time to fit residues: 263.6908 Evaluate side-chains 300 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain e residue 126 LYS Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 238 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 115 ASN B 246 GLN C 115 ASN D 115 ASN D 121 GLN D 173 HIS B D 314 GLN E 115 ASN E 121 GLN E 246 GLN a 16 ASN a 133 HIS b 8 ASN b 16 ASN b 133 HIS c 8 ASN c 133 HIS e 46 GLN e 133 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104439 restraints weight = 59605.173| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.22 r_work: 0.2898 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21445 Z= 0.288 Angle : 0.854 10.712 29060 Z= 0.450 Chirality : 0.057 0.253 3270 Planarity : 0.007 0.075 3690 Dihedral : 7.434 103.906 2955 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.13 % Allowed : 6.14 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2615 helix: 0.04 (0.16), residues: 1045 sheet: 0.22 (0.23), residues: 540 loop : 1.23 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 196 TYR 0.021 0.003 TYR A 69 PHE 0.025 0.003 PHE B 90 TRP 0.024 0.004 TRP C 340 HIS 0.007 0.003 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00640 (21445) covalent geometry : angle 0.85409 (29060) hydrogen bonds : bond 0.07906 ( 1015) hydrogen bonds : angle 5.63980 ( 2805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8796 (mttp) cc_final: 0.8483 (mmtm) REVERT: A 167 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8500 (mm-30) REVERT: B 68 LYS cc_start: 0.8884 (mttp) cc_final: 0.8562 (mmtm) REVERT: B 167 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: B 355 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: B 372 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7445 (mtm110) REVERT: C 68 LYS cc_start: 0.8898 (mttp) cc_final: 0.8545 (mmtm) REVERT: C 167 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: D 68 LYS cc_start: 0.8860 (mttp) cc_final: 0.8498 (mmtm) REVERT: D 113 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8149 (mtmt) REVERT: D 326 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8620 (ttmt) REVERT: E 68 LYS cc_start: 0.8835 (mttp) cc_final: 0.8403 (mmtm) REVERT: E 359 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.6979 (tptt) REVERT: a 30 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8073 (mtpt) REVERT: a 78 ASN cc_start: 0.8648 (m-40) cc_final: 0.7983 (p0) REVERT: b 78 ASN cc_start: 0.8670 (m-40) cc_final: 0.7979 (p0) REVERT: b 144 LYS cc_start: 0.8440 (tttm) cc_final: 0.8200 (ttpm) REVERT: c 92 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7822 (mtmm) REVERT: c 146 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.7877 (ptm160) REVERT: d 31 LYS cc_start: 0.7703 (mmpt) cc_final: 0.7143 (mppt) REVERT: d 146 ARG cc_start: 0.8141 (ptm-80) cc_final: 0.7757 (ptm160) REVERT: e 28 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6685 (mt-10) REVERT: e 31 LYS cc_start: 0.7284 (mmpt) cc_final: 0.6691 (mppt) REVERT: e 112 LYS cc_start: 0.8539 (tttp) cc_final: 0.8261 (ttpt) outliers start: 26 outliers final: 6 residues processed: 303 average time/residue: 0.7557 time to fit residues: 254.1980 Evaluate side-chains 286 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain e residue 111 LEU Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 115 ASN B 246 GLN D 115 ASN D 121 GLN D 314 GLN E 121 GLN E 246 GLN a 16 ASN b 8 ASN b 16 ASN c 8 ASN c 16 ASN e 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108774 restraints weight = 68739.975| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.47 r_work: 0.2934 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21445 Z= 0.141 Angle : 0.640 7.610 29060 Z= 0.330 Chirality : 0.047 0.190 3270 Planarity : 0.004 0.030 3690 Dihedral : 6.776 91.200 2955 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.96 % Allowed : 6.88 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2615 helix: 0.42 (0.16), residues: 1050 sheet: 0.37 (0.23), residues: 565 loop : 1.34 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 210 TYR 0.012 0.001 TYR A 69 PHE 0.016 0.002 PHE A 90 TRP 0.016 0.002 TRP B 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00289 (21445) covalent geometry : angle 0.64043 (29060) hydrogen bonds : bond 0.05284 ( 1015) hydrogen bonds : angle 5.15381 ( 2805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 291 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8786 (mttp) cc_final: 0.8472 (mmtm) REVERT: B 68 LYS cc_start: 0.8884 (mttp) cc_final: 0.8555 (mmtm) REVERT: B 372 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7386 (mtm110) REVERT: C 68 LYS cc_start: 0.8867 (mttp) cc_final: 0.8521 (mmtm) REVERT: D 68 LYS cc_start: 0.8862 (mttp) cc_final: 0.8510 (mmtm) REVERT: D 314 GLN cc_start: 0.9183 (tp40) cc_final: 0.8767 (tp-100) REVERT: E 68 LYS cc_start: 0.8811 (mttp) cc_final: 0.8386 (mmtm) REVERT: a 78 ASN cc_start: 0.8633 (m-40) cc_final: 0.7962 (p0) REVERT: a 107 GLU cc_start: 0.8341 (mp0) cc_final: 0.7897 (mp0) REVERT: b 78 ASN cc_start: 0.8658 (m-40) cc_final: 0.7967 (p0) REVERT: b 144 LYS cc_start: 0.8400 (tttm) cc_final: 0.8133 (ttpm) REVERT: c 92 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7732 (mtmm) REVERT: c 146 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7799 (ptm160) REVERT: d 31 LYS cc_start: 0.7634 (mmpt) cc_final: 0.7108 (mppt) REVERT: d 111 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8286 (tt) REVERT: d 146 ARG cc_start: 0.8085 (ptm-80) cc_final: 0.7632 (ptm160) REVERT: e 28 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6642 (mt-10) REVERT: e 31 LYS cc_start: 0.7200 (mmpt) cc_final: 0.6650 (mppt) REVERT: e 112 LYS cc_start: 0.8477 (tttp) cc_final: 0.8200 (ttpt) outliers start: 22 outliers final: 5 residues processed: 307 average time/residue: 0.7638 time to fit residues: 260.5426 Evaluate side-chains 282 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 276 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain d residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 251 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN B 246 GLN D 115 ASN D 121 GLN E 115 ASN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN e 46 GLN e 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107720 restraints weight = 51829.213| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.83 r_work: 0.2954 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21445 Z= 0.141 Angle : 0.636 7.603 29060 Z= 0.327 Chirality : 0.047 0.194 3270 Planarity : 0.004 0.030 3690 Dihedral : 6.722 91.297 2955 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.00 % Allowed : 7.41 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2615 helix: 0.59 (0.16), residues: 1050 sheet: 0.35 (0.23), residues: 565 loop : 1.36 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.012 0.001 TYR A 166 PHE 0.014 0.002 PHE A 90 TRP 0.015 0.002 TRP B 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00289 (21445) covalent geometry : angle 0.63599 (29060) hydrogen bonds : bond 0.05354 ( 1015) hydrogen bonds : angle 5.08625 ( 2805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8789 (mttp) cc_final: 0.8483 (mmtm) REVERT: B 68 LYS cc_start: 0.8868 (mttp) cc_final: 0.8541 (mmtm) REVERT: B 355 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: B 372 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7411 (mtm110) REVERT: C 68 LYS cc_start: 0.8851 (mttp) cc_final: 0.8537 (mmtm) REVERT: D 68 LYS cc_start: 0.8847 (mttp) cc_final: 0.8496 (mmtm) REVERT: D 113 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8112 (mtmt) REVERT: D 314 GLN cc_start: 0.9184 (tp40) cc_final: 0.8823 (tp-100) REVERT: E 68 LYS cc_start: 0.8805 (mttp) cc_final: 0.8380 (mmtm) REVERT: a 78 ASN cc_start: 0.8600 (m-40) cc_final: 0.7957 (p0) REVERT: b 78 ASN cc_start: 0.8624 (m-40) cc_final: 0.7964 (p0) REVERT: b 144 LYS cc_start: 0.8408 (tttm) cc_final: 0.8151 (ttpm) REVERT: c 92 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7719 (mtmm) REVERT: c 146 ARG cc_start: 0.8244 (ptm-80) cc_final: 0.7828 (ptm160) REVERT: d 31 LYS cc_start: 0.7636 (mmpt) cc_final: 0.7110 (mppt) REVERT: d 146 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7659 (ptm160) REVERT: e 28 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6636 (mt-10) REVERT: e 31 LYS cc_start: 0.7209 (mmpt) cc_final: 0.6663 (mppt) REVERT: e 112 LYS cc_start: 0.8489 (tttp) cc_final: 0.8199 (mtmm) outliers start: 23 outliers final: 8 residues processed: 297 average time/residue: 0.7451 time to fit residues: 246.2234 Evaluate side-chains 283 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 273 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 167 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 224 optimal weight: 0.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 115 ASN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN e 46 GLN e 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111444 restraints weight = 62110.687| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.32 r_work: 0.2980 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21445 Z= 0.106 Angle : 0.565 6.899 29060 Z= 0.287 Chirality : 0.044 0.174 3270 Planarity : 0.003 0.031 3690 Dihedral : 6.191 81.035 2955 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2615 helix: 0.77 (0.17), residues: 1055 sheet: 0.30 (0.23), residues: 565 loop : 1.41 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.010 0.001 TYR A 166 PHE 0.011 0.001 PHE A 90 TRP 0.013 0.002 TRP B 340 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00208 (21445) covalent geometry : angle 0.56508 (29060) hydrogen bonds : bond 0.04143 ( 1015) hydrogen bonds : angle 4.81938 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 288 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8801 (mttp) cc_final: 0.8487 (mmtm) REVERT: B 68 LYS cc_start: 0.8901 (mttp) cc_final: 0.8562 (mmtm) REVERT: B 372 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7403 (mtm110) REVERT: C 68 LYS cc_start: 0.8861 (mttp) cc_final: 0.8506 (mmtm) REVERT: C 113 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: D 68 LYS cc_start: 0.8868 (mttp) cc_final: 0.8491 (mmtm) REVERT: D 113 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: D 203 THR cc_start: 0.8434 (m) cc_final: 0.8159 (p) REVERT: D 314 GLN cc_start: 0.9180 (tp40) cc_final: 0.8831 (tp-100) REVERT: E 68 LYS cc_start: 0.8796 (mttp) cc_final: 0.8358 (mmtm) REVERT: a 78 ASN cc_start: 0.8624 (m-40) cc_final: 0.7953 (p0) REVERT: a 107 GLU cc_start: 0.8332 (mp0) cc_final: 0.7870 (mp0) REVERT: b 78 ASN cc_start: 0.8653 (m-40) cc_final: 0.7982 (p0) REVERT: b 144 LYS cc_start: 0.8386 (tttm) cc_final: 0.8107 (ttpm) REVERT: c 92 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7706 (mtmm) REVERT: c 146 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7812 (ptm160) REVERT: d 28 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6798 (mt-10) REVERT: d 31 LYS cc_start: 0.7629 (mmpt) cc_final: 0.7109 (mppt) REVERT: d 146 ARG cc_start: 0.8045 (ptm-80) cc_final: 0.7621 (ptm160) REVERT: e 28 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6602 (mt-10) REVERT: e 31 LYS cc_start: 0.7155 (mmpt) cc_final: 0.6607 (mppt) REVERT: e 112 LYS cc_start: 0.8488 (tttp) cc_final: 0.8262 (ttmm) outliers start: 15 outliers final: 4 residues processed: 301 average time/residue: 0.7482 time to fit residues: 250.3602 Evaluate side-chains 285 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 71 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 115 ASN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN d 54 GLN e 46 GLN e 78 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107765 restraints weight = 65752.954| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.21 r_work: 0.2924 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21445 Z= 0.193 Angle : 0.706 8.242 29060 Z= 0.366 Chirality : 0.050 0.210 3270 Planarity : 0.004 0.038 3690 Dihedral : 7.023 99.353 2955 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.96 % Allowed : 7.49 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2615 helix: 0.63 (0.16), residues: 1050 sheet: 0.20 (0.23), residues: 540 loop : 1.36 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.016 0.002 TYR D 166 PHE 0.016 0.002 PHE B 262 TRP 0.017 0.003 TRP A 340 HIS 0.005 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (21445) covalent geometry : angle 0.70650 (29060) hydrogen bonds : bond 0.06400 ( 1015) hydrogen bonds : angle 5.24006 ( 2805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8815 (mttp) cc_final: 0.8491 (mmtm) REVERT: B 68 LYS cc_start: 0.8884 (mttp) cc_final: 0.8552 (mmtm) REVERT: B 355 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: B 372 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7491 (mtm110) REVERT: C 68 LYS cc_start: 0.8877 (mttp) cc_final: 0.8535 (mmtm) REVERT: D 68 LYS cc_start: 0.8859 (mttp) cc_final: 0.8497 (mmtm) REVERT: D 115 ASN cc_start: 0.8908 (m-40) cc_final: 0.8695 (m-40) REVERT: D 314 GLN cc_start: 0.9214 (tp40) cc_final: 0.8844 (tp-100) REVERT: E 68 LYS cc_start: 0.8820 (mttp) cc_final: 0.8374 (mmtm) REVERT: E 125 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7948 (mt-10) REVERT: a 78 ASN cc_start: 0.8624 (m-40) cc_final: 0.7993 (p0) REVERT: c 92 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7791 (mtmm) REVERT: c 146 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7862 (ptm160) REVERT: d 28 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6824 (mt-10) REVERT: d 31 LYS cc_start: 0.7668 (mmpt) cc_final: 0.7145 (mppt) REVERT: d 111 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8321 (tt) REVERT: d 146 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7676 (ptm160) REVERT: e 12 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8267 (mm) REVERT: e 28 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6588 (mt-10) REVERT: e 31 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6624 (mppt) REVERT: e 111 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7929 (tt) REVERT: e 112 LYS cc_start: 0.8502 (tttp) cc_final: 0.8229 (ttpt) outliers start: 22 outliers final: 10 residues processed: 288 average time/residue: 0.7551 time to fit residues: 242.1765 Evaluate side-chains 287 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 273 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 111 LEU Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 228 optimal weight: 9.9990 chunk 198 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN d 54 GLN e 46 GLN e 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108552 restraints weight = 62505.782| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.21 r_work: 0.2938 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21445 Z= 0.147 Angle : 0.645 7.663 29060 Z= 0.332 Chirality : 0.047 0.195 3270 Planarity : 0.004 0.029 3690 Dihedral : 6.772 92.461 2955 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2615 helix: 0.71 (0.17), residues: 1050 sheet: 0.32 (0.23), residues: 565 loop : 1.39 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.016 0.001 TYR A 166 PHE 0.014 0.002 PHE B 262 TRP 0.015 0.002 TRP A 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00305 (21445) covalent geometry : angle 0.64503 (29060) hydrogen bonds : bond 0.05436 ( 1015) hydrogen bonds : angle 5.09084 ( 2805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 277 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8815 (mttp) cc_final: 0.8492 (mmtm) REVERT: B 68 LYS cc_start: 0.8881 (mttp) cc_final: 0.8551 (mmtm) REVERT: B 372 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7431 (mtm110) REVERT: C 68 LYS cc_start: 0.8863 (mttp) cc_final: 0.8521 (mmtm) REVERT: C 113 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (mtmt) REVERT: D 68 LYS cc_start: 0.8857 (mttp) cc_final: 0.8500 (mmtm) REVERT: D 113 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8105 (mtmt) REVERT: D 115 ASN cc_start: 0.8887 (m-40) cc_final: 0.8662 (m-40) REVERT: D 314 GLN cc_start: 0.9191 (tp40) cc_final: 0.8846 (tp-100) REVERT: E 68 LYS cc_start: 0.8804 (mttp) cc_final: 0.8363 (mmtm) REVERT: E 125 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7896 (mt-10) REVERT: a 78 ASN cc_start: 0.8619 (m-40) cc_final: 0.7990 (p0) REVERT: b 144 LYS cc_start: 0.8394 (tttm) cc_final: 0.8135 (ttpm) REVERT: c 92 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7745 (mtmm) REVERT: c 146 ARG cc_start: 0.8238 (ptm-80) cc_final: 0.7833 (ptm160) REVERT: d 31 LYS cc_start: 0.7645 (mmpt) cc_final: 0.7097 (mppt) REVERT: d 146 ARG cc_start: 0.8091 (ptm-80) cc_final: 0.7660 (ptm160) REVERT: e 28 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6567 (mt-10) REVERT: e 31 LYS cc_start: 0.7225 (mmpt) cc_final: 0.6673 (mppt) REVERT: e 111 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7899 (tt) REVERT: e 112 LYS cc_start: 0.8477 (tttp) cc_final: 0.8255 (ttmm) outliers start: 15 outliers final: 11 residues processed: 288 average time/residue: 0.7283 time to fit residues: 234.1851 Evaluate side-chains 283 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 269 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain e residue 111 LEU Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 169 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN d 54 GLN e 46 GLN e 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107686 restraints weight = 63263.525| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.29 r_work: 0.2914 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21445 Z= 0.190 Angle : 0.708 8.176 29060 Z= 0.367 Chirality : 0.050 0.216 3270 Planarity : 0.004 0.036 3690 Dihedral : 7.044 98.705 2955 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.74 % Allowed : 7.89 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2615 helix: 0.62 (0.16), residues: 1050 sheet: 0.31 (0.23), residues: 565 loop : 1.35 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 210 TYR 0.019 0.002 TYR B 166 PHE 0.016 0.002 PHE C 262 TRP 0.017 0.003 TRP B 340 HIS 0.005 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00407 (21445) covalent geometry : angle 0.70850 (29060) hydrogen bonds : bond 0.06352 ( 1015) hydrogen bonds : angle 5.26592 ( 2805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 272 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8812 (mttp) cc_final: 0.8491 (mmtm) REVERT: B 68 LYS cc_start: 0.8877 (mttp) cc_final: 0.8546 (mmtm) REVERT: B 167 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: B 355 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: B 372 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7529 (mtm110) REVERT: C 68 LYS cc_start: 0.8872 (mttp) cc_final: 0.8534 (mmtm) REVERT: C 113 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8222 (mtmt) REVERT: D 68 LYS cc_start: 0.8853 (mttp) cc_final: 0.8496 (mmtm) REVERT: D 113 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8141 (mtmt) REVERT: D 115 ASN cc_start: 0.8919 (m-40) cc_final: 0.8677 (m-40) REVERT: D 314 GLN cc_start: 0.9201 (tp40) cc_final: 0.8841 (tp-100) REVERT: E 68 LYS cc_start: 0.8816 (mttp) cc_final: 0.8376 (mmtm) REVERT: E 125 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7949 (mt-10) REVERT: a 78 ASN cc_start: 0.8607 (m-40) cc_final: 0.7983 (p0) REVERT: b 144 LYS cc_start: 0.8409 (tttm) cc_final: 0.8153 (ttpm) REVERT: c 92 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7806 (mtmm) REVERT: c 146 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.7887 (ptm160) REVERT: d 31 LYS cc_start: 0.7691 (mmpt) cc_final: 0.7151 (mppt) REVERT: d 146 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7679 (ptm160) REVERT: e 28 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6622 (mt-10) REVERT: e 31 LYS cc_start: 0.7274 (mmpt) cc_final: 0.6727 (mppt) REVERT: e 111 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7907 (tt) outliers start: 17 outliers final: 10 residues processed: 284 average time/residue: 0.7307 time to fit residues: 231.3635 Evaluate side-chains 282 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain e residue 111 LEU Chi-restraints excluded: chain e residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 155 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 198 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 233 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN b 78 ASN c 8 ASN c 16 ASN e 46 GLN e 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110493 restraints weight = 65158.470| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.29 r_work: 0.2955 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21445 Z= 0.123 Angle : 0.602 7.318 29060 Z= 0.308 Chirality : 0.046 0.182 3270 Planarity : 0.003 0.029 3690 Dihedral : 6.512 87.669 2955 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.57 % Allowed : 8.15 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2615 helix: 0.78 (0.17), residues: 1055 sheet: 0.31 (0.23), residues: 565 loop : 1.43 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.016 0.001 TYR A 166 PHE 0.011 0.001 PHE C 262 TRP 0.015 0.002 TRP B 340 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00246 (21445) covalent geometry : angle 0.60157 (29060) hydrogen bonds : bond 0.04734 ( 1015) hydrogen bonds : angle 4.95430 ( 2805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 270 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8810 (mttp) cc_final: 0.8479 (mmtm) REVERT: B 68 LYS cc_start: 0.8887 (mttp) cc_final: 0.8549 (mmtm) REVERT: B 372 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7417 (mtm110) REVERT: C 68 LYS cc_start: 0.8863 (mttp) cc_final: 0.8538 (mmtm) REVERT: C 113 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8142 (mtmt) REVERT: D 68 LYS cc_start: 0.8870 (mttp) cc_final: 0.8514 (mmtm) REVERT: D 113 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8070 (mtmt) REVERT: D 115 ASN cc_start: 0.8885 (m-40) cc_final: 0.8655 (m-40) REVERT: D 314 GLN cc_start: 0.9188 (tp40) cc_final: 0.8858 (tp-100) REVERT: E 68 LYS cc_start: 0.8799 (mttp) cc_final: 0.8356 (mmtm) REVERT: E 125 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7906 (mt-10) REVERT: a 78 ASN cc_start: 0.8619 (m-40) cc_final: 0.7987 (p0) REVERT: b 78 ASN cc_start: 0.8631 (m-40) cc_final: 0.7948 (p0) REVERT: b 144 LYS cc_start: 0.8379 (tttm) cc_final: 0.8111 (ttpm) REVERT: c 92 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7724 (mtmm) REVERT: c 146 ARG cc_start: 0.8227 (ptm-80) cc_final: 0.7833 (ptm160) REVERT: d 31 LYS cc_start: 0.7633 (mmpt) cc_final: 0.7080 (mppt) REVERT: d 146 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7630 (ptm160) REVERT: e 31 LYS cc_start: 0.7201 (mmpt) cc_final: 0.6649 (mppt) REVERT: e 111 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7886 (tt) outliers start: 13 outliers final: 9 residues processed: 280 average time/residue: 0.7406 time to fit residues: 230.8041 Evaluate side-chains 279 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain e residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 205 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 121 GLN E 121 GLN E 246 GLN b 8 ASN b 16 ASN c 8 ASN c 16 ASN e 46 GLN e 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109110 restraints weight = 60236.272| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.17 r_work: 0.2950 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21445 Z= 0.136 Angle : 0.624 7.499 29060 Z= 0.320 Chirality : 0.047 0.189 3270 Planarity : 0.004 0.029 3690 Dihedral : 6.617 89.613 2955 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.70 % Allowed : 8.19 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2615 helix: 0.80 (0.17), residues: 1050 sheet: 0.31 (0.23), residues: 565 loop : 1.42 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.015 0.001 TYR A 166 PHE 0.012 0.001 PHE B 262 TRP 0.015 0.002 TRP A 340 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00276 (21445) covalent geometry : angle 0.62398 (29060) hydrogen bonds : bond 0.05145 ( 1015) hydrogen bonds : angle 5.00991 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14088.05 seconds wall clock time: 238 minutes 56.82 seconds (14336.82 seconds total)