Starting phenix.real_space_refine on Fri Dec 8 16:26:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/12_2023/7yk7_33889_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5590 2.51 5 N 1495 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 309": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8760 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1737 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2191 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IYM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG R 194 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG R 194 " occ=0.50 Time building chain proxies: 5.09, per 1000 atoms: 0.58 Number of scatterers: 8760 At special positions: 0 Unit cell: (93.177, 118.881, 136.017, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1620 8.00 N 1495 7.00 C 5590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 33.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'I' and resid 7 through 31 Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 213 through 216 Processing helix chain 'I' and resid 228 through 230 No H-bonds generated for 'chain 'I' and resid 228 through 230' Processing helix chain 'I' and resid 243 through 255 Processing helix chain 'I' and resid 276 through 281 removed outlier: 3.501A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 276 through 281' Processing helix chain 'I' and resid 302 through 310 Processing helix chain 'I' and resid 332 through 351 Processing helix chain 'R' and resid 36 through 63 removed outlier: 3.764A pdb=" N ARG R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 102 removed outlier: 3.785A pdb=" N THR R 78 " --> pdb=" O PRO R 75 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE R 79 " --> pdb=" O SER R 76 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.558A pdb=" N SER R 101 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 144 removed outlier: 3.743A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 172 removed outlier: 3.554A pdb=" N VAL R 172 " --> pdb=" O ALA R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 178 No H-bonds generated for 'chain 'R' and resid 175 through 178' Processing helix chain 'R' and resid 200 through 212 Processing helix chain 'R' and resid 214 through 232 Processing helix chain 'R' and resid 238 through 272 removed outlier: 3.563A pdb=" N VAL R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 3.631A pdb=" N VAL R 265 " --> pdb=" O PRO R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 289 removed outlier: 4.112A pdb=" N THR R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 310 removed outlier: 3.504A pdb=" N SER R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN R 301 " --> pdb=" O LEU R 297 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS R 303 " --> pdb=" O HIS R 299 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 314 through 321 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.632A pdb=" N CYS T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 35 Processing sheet with id= A, first strand: chain 'I' and resid 320 through 324 removed outlier: 6.459A pdb=" N ILE I 265 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.847A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 17 through 20 removed outlier: 3.559A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 95 through 99 Processing sheet with id= E, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= F, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= G, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.369A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= I, first strand: chain 'T' and resid 58 through 63 removed outlier: 6.749A pdb=" N ALA T 73 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET T 61 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL T 71 " --> pdb=" O MET T 61 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP T 63 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU T 69 " --> pdb=" O TRP T 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS T 91 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP T 83 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS T 89 " --> pdb=" O ASP T 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 100 through 105 removed outlier: 7.021A pdb=" N GLY T 115 " --> pdb=" O MET T 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS T 103 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA T 113 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR T 105 " --> pdb=" O TYR T 111 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR T 111 " --> pdb=" O TYR T 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU T 139 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG T 137 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN T 125 " --> pdb=" O VAL T 135 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL T 135 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.657A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 220 through 222 removed outlier: 4.136A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER T 207 " --> pdb=" O ALA T 203 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 229 through 234 removed outlier: 6.920A pdb=" N GLY T 244 " --> pdb=" O ASN T 230 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE T 232 " --> pdb=" O ALA T 242 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA T 242 " --> pdb=" O ILE T 232 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE T 234 " --> pdb=" O ALA T 240 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA T 240 " --> pdb=" O PHE T 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET T 262 " --> pdb=" O LEU T 252 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP T 254 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU T 260 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 273 through 278 removed outlier: 6.646A pdb=" N GLY T 288 " --> pdb=" O THR T 274 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL T 276 " --> pdb=" O LEU T 286 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU T 286 " --> pdb=" O VAL T 276 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE T 278 " --> pdb=" O LEU T 284 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU T 284 " --> pdb=" O PHE T 278 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY T 306 " --> pdb=" O VAL T 296 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP T 298 " --> pdb=" O ARG T 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG T 304 " --> pdb=" O ASP T 298 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 47 through 51 removed outlier: 6.863A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 912 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: 2.55 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1412 1.31 - 1.43: 2459 1.43 - 1.56: 5001 1.56 - 1.68: 3 1.68 - 1.81: 78 Bond restraints: 8953 Sorted by residual: bond pdb=" C26 IYM R 401 " pdb=" C36 IYM R 401 " ideal model delta sigma weight residual 1.365 1.444 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C24 IYM R 401 " pdb=" C25 IYM R 401 " ideal model delta sigma weight residual 1.532 1.596 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C15 IYM R 401 " pdb=" N14 IYM R 401 " ideal model delta sigma weight residual 1.465 1.529 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C25 IYM R 401 " pdb=" C26 IYM R 401 " ideal model delta sigma weight residual 1.529 1.591 -0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" CA ARG I 243 " pdb=" C ARG I 243 " ideal model delta sigma weight residual 1.522 1.484 0.039 1.36e-02 5.41e+03 8.17e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 95.50 - 103.20: 62 103.20 - 110.90: 3189 110.90 - 118.60: 3825 118.60 - 126.30: 4915 126.30 - 134.00: 160 Bond angle restraints: 12151 Sorted by residual: angle pdb=" N LEU I 233 " pdb=" CA LEU I 233 " pdb=" C LEU I 233 " ideal model delta sigma weight residual 109.11 95.50 13.61 1.42e+00 4.96e-01 9.19e+01 angle pdb=" C25 IYM R 401 " pdb=" C26 IYM R 401 " pdb=" C27 IYM R 401 " ideal model delta sigma weight residual 105.72 126.26 -20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" N VAL I 234 " pdb=" CA VAL I 234 " pdb=" C VAL I 234 " ideal model delta sigma weight residual 109.34 120.11 -10.77 2.08e+00 2.31e-01 2.68e+01 angle pdb=" C25 IYM R 401 " pdb=" C26 IYM R 401 " pdb=" C36 IYM R 401 " ideal model delta sigma weight residual 143.07 127.93 15.14 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C SER R 197 " pdb=" N ARG R 198 " pdb=" CA ARG R 198 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 ... (remaining 12146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 4916 21.73 - 43.46: 310 43.46 - 65.19: 22 65.19 - 86.92: 11 86.92 - 108.65: 6 Dihedral angle restraints: 5265 sinusoidal: 2025 harmonic: 3240 Sorted by residual: dihedral pdb=" CA PRO R 196 " pdb=" C PRO R 196 " pdb=" N SER R 197 " pdb=" CA SER R 197 " ideal model delta harmonic sigma weight residual 180.00 144.50 35.50 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA LYS S 163 " pdb=" C LYS S 163 " pdb=" N SER S 164 " pdb=" CA SER S 164 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 5262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1076 0.056 - 0.113: 277 0.113 - 0.169: 23 0.169 - 0.226: 2 0.226 - 0.282: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA LEU I 233 " pdb=" N LEU I 233 " pdb=" C LEU I 233 " pdb=" CB LEU I 233 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ARG R 198 " pdb=" N ARG R 198 " pdb=" C ARG R 198 " pdb=" CB ARG R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ILE T 273 " pdb=" N ILE T 273 " pdb=" C ILE T 273 " pdb=" CB ILE T 273 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1376 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 197 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C SER R 197 " 0.054 2.00e-02 2.50e+03 pdb=" O SER R 197 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG R 198 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 289 " -0.010 2.00e-02 2.50e+03 1.32e-02 3.47e+00 pdb=" CG TYR T 289 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 289 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR T 289 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 289 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR T 289 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR T 289 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 289 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO G 49 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.024 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 145 2.67 - 3.23: 8529 3.23 - 3.79: 13537 3.79 - 4.34: 17602 4.34 - 4.90: 29931 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" O HIS R 299 " pdb=" OG SER R 302 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASN R 82 " pdb=" OG1 THR R 162 " model vdw 2.179 2.440 nonbonded pdb=" OE2 GLU I 8 " pdb=" OH TYR S 175 " model vdw 2.188 2.440 nonbonded pdb=" NZ LYS I 272 " pdb=" O THR I 325 " model vdw 2.198 2.520 nonbonded pdb=" O ILE T 58 " pdb=" OG SER T 316 " model vdw 2.236 2.440 ... (remaining 69739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.840 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.760 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 0.079 8953 Z= 0.366 Angle : 0.799 20.544 12151 Z= 0.412 Chirality : 0.047 0.282 1379 Planarity : 0.004 0.043 1533 Dihedral : 14.121 108.646 3169 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.11 % Allowed : 0.85 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1104 helix: 1.55 (0.27), residues: 377 sheet: -0.44 (0.33), residues: 267 loop : -1.64 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 200 HIS 0.009 0.001 HIS T 183 PHE 0.018 0.002 PHE T 235 TYR 0.027 0.002 TYR T 289 ARG 0.009 0.001 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 1.1717 time to fit residues: 268.4000 Evaluate side-chains 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN T 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8953 Z= 0.245 Angle : 0.648 9.318 12151 Z= 0.330 Chirality : 0.045 0.233 1379 Planarity : 0.005 0.039 1533 Dihedral : 9.069 108.302 1227 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.35 % Allowed : 12.15 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1104 helix: 1.32 (0.27), residues: 375 sheet: -0.46 (0.32), residues: 280 loop : -1.53 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 82 HIS 0.006 0.001 HIS T 183 PHE 0.024 0.002 PHE R 230 TYR 0.016 0.001 TYR R 309 ARG 0.007 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 220 average time/residue: 1.1591 time to fit residues: 272.2703 Evaluate side-chains 207 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.3716 time to fit residues: 4.0475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.3980 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 108 optimal weight: 0.0370 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 overall best weight: 0.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 HIS T 175 GLN T 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8953 Z= 0.150 Angle : 0.580 8.135 12151 Z= 0.293 Chirality : 0.042 0.243 1379 Planarity : 0.004 0.043 1533 Dihedral : 8.860 107.090 1227 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.88 % Allowed : 16.95 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1104 helix: 1.45 (0.28), residues: 368 sheet: -0.19 (0.32), residues: 273 loop : -1.46 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 82 HIS 0.003 0.001 HIS T 183 PHE 0.023 0.001 PHE R 230 TYR 0.007 0.001 TYR R 309 ARG 0.010 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 226 average time/residue: 1.0455 time to fit residues: 253.8146 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 9 average time/residue: 0.1400 time to fit residues: 3.2825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 110 ASN T 119 ASN T 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8953 Z= 0.194 Angle : 0.589 8.215 12151 Z= 0.297 Chirality : 0.043 0.232 1379 Planarity : 0.004 0.037 1533 Dihedral : 8.712 107.237 1227 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.99 % Allowed : 20.26 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1104 helix: 1.52 (0.28), residues: 364 sheet: -0.15 (0.32), residues: 273 loop : -1.42 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.019 0.001 PHE R 230 TYR 0.012 0.001 TYR S 60 ARG 0.008 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 199 average time/residue: 1.0458 time to fit residues: 223.9066 Evaluate side-chains 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.5985 time to fit residues: 5.3907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.0050 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN T 175 GLN T 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8953 Z= 0.197 Angle : 0.585 8.048 12151 Z= 0.296 Chirality : 0.043 0.230 1379 Planarity : 0.004 0.040 1533 Dihedral : 8.701 107.207 1227 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.05 % Allowed : 19.83 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1104 helix: 1.47 (0.28), residues: 364 sheet: -0.20 (0.32), residues: 276 loop : -1.32 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 PHE 0.017 0.001 PHE R 230 TYR 0.014 0.001 TYR S 60 ARG 0.007 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 207 average time/residue: 1.0191 time to fit residues: 227.7821 Evaluate side-chains 198 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 9 average time/residue: 0.4902 time to fit residues: 6.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 55 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN T 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8953 Z= 0.169 Angle : 0.581 9.064 12151 Z= 0.290 Chirality : 0.042 0.222 1379 Planarity : 0.004 0.041 1533 Dihedral : 8.661 106.817 1227 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.77 % Allowed : 21.96 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1104 helix: 1.58 (0.28), residues: 363 sheet: -0.05 (0.32), residues: 277 loop : -1.34 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.004 0.000 HIS T 183 PHE 0.015 0.001 PHE R 230 TYR 0.013 0.001 TYR S 60 ARG 0.006 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.079 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 203 average time/residue: 1.0107 time to fit residues: 221.0817 Evaluate side-chains 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.2114 time to fit residues: 3.6109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.0040 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN ** T 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8953 Z= 0.194 Angle : 0.598 9.227 12151 Z= 0.298 Chirality : 0.043 0.219 1379 Planarity : 0.004 0.044 1533 Dihedral : 8.688 106.640 1227 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.77 % Allowed : 23.13 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1104 helix: 1.59 (0.28), residues: 363 sheet: 0.01 (0.31), residues: 290 loop : -1.41 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 82 HIS 0.003 0.001 HIS T 183 PHE 0.014 0.001 PHE R 230 TYR 0.012 0.001 TYR S 60 ARG 0.008 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 0.945 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 200 average time/residue: 1.0098 time to fit residues: 217.6730 Evaluate side-chains 195 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.2398 time to fit residues: 3.4762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 305 ASN T 110 ASN ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8953 Z= 0.254 Angle : 0.630 10.401 12151 Z= 0.315 Chirality : 0.044 0.222 1379 Planarity : 0.004 0.045 1533 Dihedral : 8.728 107.157 1227 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.88 % Allowed : 23.56 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1104 helix: 1.51 (0.28), residues: 369 sheet: 0.04 (0.31), residues: 294 loop : -1.39 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.015 0.002 PHE I 197 TYR 0.013 0.001 TYR S 190 ARG 0.008 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.002 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 206 average time/residue: 1.1529 time to fit residues: 253.7386 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.1224 time to fit residues: 2.9214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 77 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN T 220 GLN ** T 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8953 Z= 0.244 Angle : 0.646 12.001 12151 Z= 0.319 Chirality : 0.044 0.219 1379 Planarity : 0.004 0.046 1533 Dihedral : 8.809 106.555 1227 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.24 % Allowed : 24.84 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1104 helix: 1.47 (0.28), residues: 370 sheet: 0.06 (0.31), residues: 294 loop : -1.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.013 0.001 PHE R 230 TYR 0.014 0.001 TYR S 190 ARG 0.008 0.000 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.980 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 204 average time/residue: 1.1395 time to fit residues: 248.2826 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.2750 time to fit residues: 3.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 9 optimal weight: 0.0000 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 110 ASN T 155 ASN T 175 GLN T 239 ASN T 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8953 Z= 0.206 Angle : 0.639 12.602 12151 Z= 0.315 Chirality : 0.043 0.216 1379 Planarity : 0.004 0.048 1533 Dihedral : 8.834 106.056 1227 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.71 % Allowed : 26.12 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1104 helix: 1.52 (0.28), residues: 370 sheet: 0.18 (0.31), residues: 287 loop : -1.45 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.013 0.001 PHE R 230 TYR 0.011 0.001 TYR S 190 ARG 0.008 0.000 ARG T 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 0.996 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 190 average time/residue: 1.2281 time to fit residues: 248.7604 Evaluate side-chains 196 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 5 average time/residue: 0.1622 time to fit residues: 2.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127738 restraints weight = 12618.475| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.17 r_work: 0.3686 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8953 Z= 0.204 Angle : 0.637 12.653 12151 Z= 0.316 Chirality : 0.043 0.212 1379 Planarity : 0.004 0.050 1533 Dihedral : 8.759 105.587 1227 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 25.59 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1104 helix: 1.62 (0.28), residues: 365 sheet: 0.18 (0.31), residues: 282 loop : -1.44 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.012 0.001 PHE R 230 TYR 0.012 0.001 TYR S 60 ARG 0.008 0.000 ARG T 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.73 seconds wall clock time: 76 minutes 20.47 seconds (4580.47 seconds total)