Starting phenix.real_space_refine on Wed Feb 14 06:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_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_33889/02_2024/7yk7_33889_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_33889_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk7_33889/02_2024/7yk7_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-dev-5238/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: 5.06, 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: 3.11 Conformation dependent library (CDL) restraints added in 1.4 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: 1.86 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: 2.67 Time building geometry restraints manager: 3.35 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: 1.290 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: 0.000 Extract box with map and model: 3.780 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.780 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.010 ------------------------------------------------------------------------------- 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 : 0.954 Fit side-chains revert: symmetry clash REVERT: I 43 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: I 272 LYS cc_start: 0.8073 (pttm) cc_final: 0.7658 (pmtt) REVERT: R 249 ARG cc_start: 0.6839 (tpm170) cc_final: 0.6605 (tpm170) REVERT: S 220 GLU cc_start: 0.7335 (mp0) cc_final: 0.6714 (mp0) REVERT: S 224 VAL cc_start: 0.8272 (t) cc_final: 0.7994 (p) REVERT: T 38 ASP cc_start: 0.7523 (p0) cc_final: 0.7226 (p0) REVERT: T 50 THR cc_start: 0.8574 (m) cc_final: 0.8251 (t) REVERT: T 61 MET cc_start: 0.7240 (ppp) cc_final: 0.6943 (ppp) REVERT: T 76 ASP cc_start: 0.6688 (p0) cc_final: 0.6458 (p0) REVERT: T 96 ARG cc_start: 0.6727 (mtt90) cc_final: 0.6502 (mtt90) REVERT: T 97 SER cc_start: 0.8130 (t) cc_final: 0.7806 (t) REVERT: T 120 ILE cc_start: 0.8055 (mp) cc_final: 0.7846 (mt) REVERT: T 227 SER cc_start: 0.7930 (m) cc_final: 0.7544 (m) REVERT: T 247 ASP cc_start: 0.6710 (m-30) cc_final: 0.6370 (m-30) REVERT: T 254 ASP cc_start: 0.7136 (t70) cc_final: 0.6927 (t70) REVERT: T 268 ASN cc_start: 0.7131 (t0) cc_final: 0.6919 (t0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 1.1499 time to fit residues: 263.3672 Evaluate side-chains 197 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU 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: 0.8980 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: 0.0010 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8953 Z= 0.249 Angle : 0.645 9.615 12151 Z= 0.329 Chirality : 0.044 0.237 1379 Planarity : 0.005 0.039 1533 Dihedral : 9.369 108.044 1230 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.13 % Allowed : 11.51 % Favored : 86.35 % 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: -0.40 (0.26), residues: 1104 helix: 1.35 (0.27), residues: 375 sheet: -0.43 (0.31), residues: 286 loop : -1.56 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.006 0.001 HIS T 183 PHE 0.023 0.002 PHE R 230 TYR 0.015 0.001 TYR R 309 ARG 0.006 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 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: I 33 GLU cc_start: 0.6854 (tp30) cc_final: 0.6443 (tp30) REVERT: I 43 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: I 272 LYS cc_start: 0.8089 (pttm) cc_final: 0.7678 (pmtt) REVERT: R 249 ARG cc_start: 0.6823 (tpm170) cc_final: 0.6545 (tpm170) REVERT: S 192 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4549 (tpt) REVERT: S 220 GLU cc_start: 0.7376 (mp0) cc_final: 0.6751 (mp0) REVERT: S 224 VAL cc_start: 0.8197 (t) cc_final: 0.7904 (p) REVERT: T 38 ASP cc_start: 0.7569 (p0) cc_final: 0.7240 (p0) REVERT: T 254 ASP cc_start: 0.7185 (t70) cc_final: 0.6969 (t70) REVERT: T 268 ASN cc_start: 0.7093 (t0) cc_final: 0.6893 (t0) REVERT: T 270 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8038 (pp) outliers start: 20 outliers final: 12 residues processed: 216 average time/residue: 1.1676 time to fit residues: 269.2574 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.0060 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN T 62 HIS T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8953 Z= 0.197 Angle : 0.596 8.243 12151 Z= 0.302 Chirality : 0.043 0.239 1379 Planarity : 0.005 0.037 1533 Dihedral : 9.159 107.270 1230 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.99 % Allowed : 15.67 % Favored : 81.34 % 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: -0.32 (0.26), residues: 1104 helix: 1.34 (0.28), residues: 375 sheet: -0.26 (0.32), residues: 273 loop : -1.49 (0.28), residues: 456 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 0.026 0.001 PHE R 230 TYR 0.015 0.001 TYR R 309 ARG 0.007 0.000 ARG S 191 *********************** 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 238 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: I 26 ASP cc_start: 0.7037 (t0) cc_final: 0.6684 (t0) REVERT: I 33 GLU cc_start: 0.6857 (tp30) cc_final: 0.6451 (tp30) REVERT: I 272 LYS cc_start: 0.8136 (pttm) cc_final: 0.7730 (pmtt) REVERT: R 249 ARG cc_start: 0.6777 (tpm170) cc_final: 0.6467 (tpm170) REVERT: S 174 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7638 (tp) REVERT: S 192 MET cc_start: 0.4643 (OUTLIER) cc_final: 0.4257 (tpt) REVERT: S 220 GLU cc_start: 0.7387 (mp0) cc_final: 0.6834 (mp0) REVERT: T 90 VAL cc_start: 0.8108 (t) cc_final: 0.7907 (t) REVERT: T 155 ASN cc_start: 0.7355 (t0) cc_final: 0.7083 (t0) REVERT: T 268 ASN cc_start: 0.7089 (t0) cc_final: 0.6879 (t0) REVERT: T 270 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8048 (pp) outliers start: 28 outliers final: 13 residues processed: 217 average time/residue: 1.0542 time to fit residues: 245.2476 Evaluate side-chains 215 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 119 ASN T 175 GLN T 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8953 Z= 0.254 Angle : 0.602 8.233 12151 Z= 0.305 Chirality : 0.044 0.233 1379 Planarity : 0.004 0.036 1533 Dihedral : 8.786 107.579 1227 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.16 % Allowed : 17.70 % Favored : 78.14 % 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: 1.32 (0.28), residues: 373 sheet: -0.34 (0.32), residues: 278 loop : -1.48 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 PHE 0.020 0.002 PHE R 230 TYR 0.015 0.001 TYR R 309 ARG 0.006 0.000 ARG T 129 *********************** 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 250 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 0.869 Fit side-chains REVERT: I 26 ASP cc_start: 0.7030 (t0) cc_final: 0.6681 (t0) REVERT: I 33 GLU cc_start: 0.6880 (tp30) cc_final: 0.6493 (tp30) REVERT: I 226 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7866 (m) REVERT: I 272 LYS cc_start: 0.8161 (pttm) cc_final: 0.7727 (pmtt) REVERT: R 249 ARG cc_start: 0.6773 (tpm170) cc_final: 0.6424 (tpm170) REVERT: S 192 MET cc_start: 0.4836 (tpt) cc_final: 0.4412 (tpt) REVERT: S 220 GLU cc_start: 0.7423 (mp0) cc_final: 0.6924 (mp0) REVERT: T 90 VAL cc_start: 0.8119 (t) cc_final: 0.7917 (t) REVERT: T 268 ASN cc_start: 0.7055 (t0) cc_final: 0.6840 (t0) REVERT: T 270 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (pp) outliers start: 39 outliers final: 21 residues processed: 227 average time/residue: 1.0535 time to fit residues: 256.3130 Evaluate side-chains 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.0170 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 T 175 GLN T 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8953 Z= 0.264 Angle : 0.605 8.133 12151 Z= 0.307 Chirality : 0.044 0.232 1379 Planarity : 0.004 0.036 1533 Dihedral : 8.784 107.816 1227 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.80 % Allowed : 18.76 % Favored : 76.44 % 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: -0.31 (0.26), residues: 1104 helix: 1.32 (0.28), residues: 370 sheet: -0.28 (0.31), residues: 284 loop : -1.44 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 PHE 0.017 0.001 PHE R 230 TYR 0.013 0.001 TYR S 190 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 245 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 0.904 Fit side-chains REVERT: I 26 ASP cc_start: 0.7035 (t0) cc_final: 0.6684 (t0) REVERT: I 33 GLU cc_start: 0.6896 (tp30) cc_final: 0.6675 (tp30) REVERT: I 199 MET cc_start: 0.7647 (mtp) cc_final: 0.7401 (mtm) REVERT: I 226 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7851 (m) REVERT: I 272 LYS cc_start: 0.8183 (pttm) cc_final: 0.7756 (pmtt) REVERT: R 249 ARG cc_start: 0.6789 (tpm170) cc_final: 0.6414 (tpm170) REVERT: S 174 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7706 (tt) REVERT: S 220 GLU cc_start: 0.7421 (mp0) cc_final: 0.6917 (mp0) REVERT: T 90 VAL cc_start: 0.8121 (t) cc_final: 0.7921 (t) REVERT: T 119 ASN cc_start: 0.7616 (m-40) cc_final: 0.7388 (m-40) REVERT: T 268 ASN cc_start: 0.7045 (t0) cc_final: 0.6810 (t0) REVERT: T 270 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (pp) outliers start: 45 outliers final: 23 residues processed: 218 average time/residue: 1.0539 time to fit residues: 246.4225 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN T 110 ASN T 142 HIS T 155 ASN T 175 GLN T 220 GLN T 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8953 Z= 0.414 Angle : 0.667 10.749 12151 Z= 0.342 Chirality : 0.047 0.231 1379 Planarity : 0.005 0.041 1533 Dihedral : 8.941 108.157 1227 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.12 % Allowed : 20.79 % Favored : 74.09 % 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: -0.56 (0.25), residues: 1104 helix: 1.10 (0.27), residues: 369 sheet: -0.37 (0.30), residues: 294 loop : -1.62 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 82 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.002 PHE T 151 TYR 0.021 0.002 TYR S 190 ARG 0.007 0.001 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 257 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.002 Fit side-chains REVERT: I 33 GLU cc_start: 0.6876 (tp30) cc_final: 0.6651 (tp30) REVERT: I 43 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: I 233 LEU cc_start: 0.8376 (mm) cc_final: 0.7947 (mp) REVERT: I 256 ASN cc_start: 0.8245 (m-40) cc_final: 0.7888 (m-40) REVERT: I 272 LYS cc_start: 0.8201 (pttm) cc_final: 0.7819 (pmtt) REVERT: R 249 ARG cc_start: 0.6897 (tpm170) cc_final: 0.6542 (tpm170) REVERT: S 174 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7783 (tt) REVERT: S 220 GLU cc_start: 0.7422 (mp0) cc_final: 0.6819 (mp0) REVERT: S 224 VAL cc_start: 0.8266 (t) cc_final: 0.8050 (p) REVERT: T 119 ASN cc_start: 0.7667 (m-40) cc_final: 0.7311 (m-40) REVERT: T 268 ASN cc_start: 0.7044 (t0) cc_final: 0.6786 (t0) REVERT: T 270 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8036 (pp) outliers start: 48 outliers final: 31 residues processed: 233 average time/residue: 0.9754 time to fit residues: 245.9912 Evaluate side-chains 238 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 0.0040 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 347 ASN S 3 GLN T 142 HIS T 175 GLN T 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1962 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= 0.206 Angle : 0.612 13.132 12151 Z= 0.306 Chirality : 0.043 0.222 1379 Planarity : 0.004 0.038 1533 Dihedral : 8.871 105.941 1227 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.73 % Allowed : 23.88 % Favored : 72.39 % 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: 1.41 (0.28), residues: 362 sheet: -0.21 (0.31), residues: 295 loop : -1.42 (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 0.026 0.001 PHE R 256 TYR 0.013 0.001 TYR S 60 ARG 0.007 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 237 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 0.859 Fit side-chains REVERT: I 33 GLU cc_start: 0.6876 (tp30) cc_final: 0.6500 (tp30) REVERT: I 43 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: I 226 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7854 (m) REVERT: I 272 LYS cc_start: 0.8188 (pttm) cc_final: 0.7858 (pmtt) REVERT: R 249 ARG cc_start: 0.6758 (tpm170) cc_final: 0.6288 (tpm170) REVERT: S 220 GLU cc_start: 0.7418 (mp0) cc_final: 0.7009 (mp0) REVERT: T 119 ASN cc_start: 0.7600 (m-40) cc_final: 0.7261 (m-40) REVERT: T 268 ASN cc_start: 0.7033 (t0) cc_final: 0.6786 (t0) REVERT: T 270 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8013 (pp) outliers start: 35 outliers final: 23 residues processed: 219 average time/residue: 1.0664 time to fit residues: 249.9871 Evaluate side-chains 225 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET 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: 0.8980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN T 75 GLN T 142 HIS T 175 GLN T 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8953 Z= 0.254 Angle : 0.629 12.108 12151 Z= 0.315 Chirality : 0.044 0.225 1379 Planarity : 0.004 0.040 1533 Dihedral : 8.820 106.273 1227 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.94 % Allowed : 23.99 % Favored : 72.07 % 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: -0.25 (0.26), residues: 1104 helix: 1.39 (0.28), residues: 363 sheet: -0.20 (0.31), residues: 289 loop : -1.42 (0.28), residues: 452 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 0.020 0.002 PHE S 212 TYR 0.016 0.001 TYR S 60 ARG 0.007 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 239 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 0.947 Fit side-chains REVERT: I 33 GLU cc_start: 0.6874 (tp30) cc_final: 0.6491 (tp30) REVERT: I 43 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: I 226 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7860 (m) REVERT: I 272 LYS cc_start: 0.8200 (pttm) cc_final: 0.7857 (pmtt) REVERT: S 220 GLU cc_start: 0.7459 (mp0) cc_final: 0.7051 (mp0) REVERT: T 119 ASN cc_start: 0.7589 (m-40) cc_final: 0.7260 (m-40) REVERT: T 268 ASN cc_start: 0.7031 (t0) cc_final: 0.6781 (t0) REVERT: T 270 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8027 (pp) REVERT: T 316 SER cc_start: 0.8017 (t) cc_final: 0.7740 (m) outliers start: 37 outliers final: 29 residues processed: 221 average time/residue: 1.0644 time to fit residues: 252.2108 Evaluate side-chains 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 75 GLN T 142 HIS T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8953 Z= 0.212 Angle : 0.618 12.674 12151 Z= 0.309 Chirality : 0.043 0.220 1379 Planarity : 0.004 0.039 1533 Dihedral : 8.806 105.739 1227 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.94 % Allowed : 24.95 % Favored : 71.11 % 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: 1.46 (0.28), residues: 363 sheet: -0.16 (0.31), residues: 295 loop : -1.39 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 PHE 0.027 0.002 PHE R 256 TYR 0.015 0.001 TYR S 60 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 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 0.879 Fit side-chains REVERT: I 33 GLU cc_start: 0.6888 (tp30) cc_final: 0.6509 (tp30) REVERT: I 43 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: I 226 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7859 (m) REVERT: I 233 LEU cc_start: 0.8458 (mt) cc_final: 0.8181 (mp) REVERT: I 272 LYS cc_start: 0.8196 (pttm) cc_final: 0.7851 (pmtt) REVERT: S 220 GLU cc_start: 0.7449 (mp0) cc_final: 0.7050 (mp0) REVERT: T 119 ASN cc_start: 0.7577 (m-40) cc_final: 0.7254 (m-40) REVERT: T 268 ASN cc_start: 0.7031 (t0) cc_final: 0.6776 (t0) REVERT: T 270 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8002 (pp) REVERT: T 316 SER cc_start: 0.8010 (t) cc_final: 0.7741 (m) outliers start: 37 outliers final: 29 residues processed: 212 average time/residue: 1.0585 time to fit residues: 240.4406 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 75 GLN T 142 HIS T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8953 Z= 0.231 Angle : 0.626 12.969 12151 Z= 0.314 Chirality : 0.044 0.220 1379 Planarity : 0.004 0.040 1533 Dihedral : 8.767 105.635 1227 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.73 % Allowed : 25.69 % Favored : 70.58 % 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: -0.13 (0.26), residues: 1104 helix: 1.57 (0.28), residues: 358 sheet: -0.16 (0.31), residues: 295 loop : -1.39 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 PHE 0.031 0.002 PHE S 212 TYR 0.014 0.001 TYR S 60 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 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.021 Fit side-chains REVERT: I 33 GLU cc_start: 0.6897 (tp30) cc_final: 0.6514 (tp30) REVERT: I 43 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: I 226 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7858 (m) REVERT: I 233 LEU cc_start: 0.8450 (mt) cc_final: 0.8205 (mp) REVERT: I 272 LYS cc_start: 0.8194 (pttm) cc_final: 0.7717 (pmtt) REVERT: S 220 GLU cc_start: 0.7435 (mp0) cc_final: 0.7042 (mp0) REVERT: T 119 ASN cc_start: 0.7581 (m-40) cc_final: 0.7257 (m-40) REVERT: T 205 ASP cc_start: 0.7107 (t70) cc_final: 0.6601 (t0) REVERT: T 268 ASN cc_start: 0.7024 (t0) cc_final: 0.6765 (t0) REVERT: T 270 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (pp) REVERT: T 316 SER cc_start: 0.8016 (t) cc_final: 0.7748 (m) outliers start: 35 outliers final: 30 residues processed: 208 average time/residue: 1.0980 time to fit residues: 244.1735 Evaluate side-chains 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 87 optimal weight: 0.0980 chunk 36 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN T 75 GLN T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.146125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128834 restraints weight = 12594.883| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.17 r_work: 0.3701 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8953 Z= 0.166 Angle : 0.606 12.867 12151 Z= 0.300 Chirality : 0.042 0.209 1379 Planarity : 0.004 0.040 1533 Dihedral : 8.671 104.436 1227 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.20 % Allowed : 26.44 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1104 helix: 1.72 (0.28), residues: 358 sheet: -0.05 (0.31), residues: 288 loop : -1.26 (0.29), residues: 458 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 0.026 0.001 PHE S 212 TYR 0.011 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: 4344.37 seconds wall clock time: 77 minutes 19.75 seconds (4639.75 seconds total)