Starting phenix.real_space_refine on Sat Aug 23 01:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj4_33871/08_2025/7yj4_33871.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.092 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 62 5.16 5 C 5726 2.51 5 N 1538 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 140 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 168 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} 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: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1662 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 3 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: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2220 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 270} 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: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 8985 At special positions: 0 Unit cell: (91.035, 119.952, 143.514, 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 62 16.00 O 1659 8.00 N 1538 7.00 C 5726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS B 19 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 407.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 38.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.922A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.689A pdb=" N LEU A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 21' Processing helix chain 'B' and resid 10 through 21 removed outlier: 4.196A pdb=" N VAL B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.892A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.626A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 31 removed outlier: 3.605A pdb=" N ASN I 22 " --> pdb=" O MET I 18 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.620A pdb=" N GLN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 217 removed outlier: 5.271A pdb=" N ILE I 213 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 217 " --> pdb=" O HIS I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.989A pdb=" N GLU I 276 " --> pdb=" O LYS I 272 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 278 " --> pdb=" O LEU I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 311 Processing helix chain 'I' and resid 331 through 352 Processing helix chain 'R' and resid 35 through 39 removed outlier: 3.855A pdb=" N ARG R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 64 removed outlier: 3.643A pdb=" N ILE R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 103 removed outlier: 3.949A pdb=" N VAL R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 4.202A pdb=" N GLU R 100 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER R 101 " --> pdb=" O TRP R 97 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 144 removed outlier: 4.267A pdb=" N LEU R 113 " --> pdb=" O PHE R 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 3.686A pdb=" N TRP R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 200 through 213 removed outlier: 3.652A pdb=" N LEU R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 233 Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.309A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 4.570A pdb=" N LYS R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 Processing helix chain 'R' and resid 289 through 300 removed outlier: 3.513A pdb=" N VAL R 293 " --> pdb=" O TYR R 289 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 297 " --> pdb=" O VAL R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix removed outlier: 3.546A pdb=" N TYR R 309 " --> pdb=" O ASN R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 324 removed outlier: 3.723A pdb=" N ARG R 317 " --> pdb=" O ARG R 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA R 319 " --> pdb=" O GLU R 315 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU R 320 " --> pdb=" O PRO R 316 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY R 322 " --> pdb=" O GLN R 318 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.780A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.664A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.647A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.852A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.893A pdb=" N ALA T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 35 through 37 No H-bonds generated for 'chain 'T' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 192 removed outlier: 3.830A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS I 225 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AA3, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.000A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.773A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 147 through 148 removed outlier: 3.803A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL S 226 " --> pdb=" O GLN S 179 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 46 through 52 removed outlier: 6.695A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER T 331 " --> pdb=" O PHE T 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 58 through 63 removed outlier: 6.761A pdb=" N ALA T 73 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET T 61 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL T 71 " --> pdb=" O MET T 61 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP T 63 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU T 69 " --> pdb=" O TRP T 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU T 70 " --> pdb=" O TRP T 82 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 104 through 105 removed outlier: 6.278A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG T 134 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.951A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 191 through 192 removed outlier: 3.622A pdb=" N SER T 201 " --> pdb=" O LYS T 209 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS T 209 " --> pdb=" O SER T 201 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 229 through 234 removed outlier: 4.169A pdb=" N SER T 245 " --> pdb=" O THR T 249 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR T 249 " --> pdb=" O SER T 245 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS T 250 " --> pdb=" O TYR T 264 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET T 262 " --> pdb=" O LEU T 252 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP T 254 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU T 260 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 276 through 278 380 hydrogen bonds defined for protein. 1059 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: 1.03 Time building geometry restraints manager: 0.86 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: 1449 1.31 - 1.44: 2570 1.44 - 1.57: 5071 1.57 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 9176 Sorted by residual: bond pdb=" CA THR R 121 " pdb=" C THR R 121 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.24e-02 6.50e+03 6.78e+01 bond pdb=" C THR R 121 " pdb=" N VAL R 122 " ideal model delta sigma weight residual 1.335 1.260 0.075 1.23e-02 6.61e+03 3.74e+01 bond pdb=" CA ASP R 104 " pdb=" C ASP R 104 " ideal model delta sigma weight residual 1.526 1.460 0.067 1.11e-02 8.12e+03 3.64e+01 bond pdb=" CA HIS R 106 " pdb=" C HIS R 106 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.21e-02 6.83e+03 3.07e+01 bond pdb=" C THR R 121 " pdb=" O THR R 121 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.16e-02 7.43e+03 2.46e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12324 2.75 - 5.50: 104 5.50 - 8.25: 13 8.25 - 10.99: 3 10.99 - 13.74: 3 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N THR R 323 " pdb=" CA THR R 323 " pdb=" C THR R 323 " ideal model delta sigma weight residual 113.97 100.23 13.74 1.28e+00 6.10e-01 1.15e+02 angle pdb=" N LEU R 267 " pdb=" CA LEU R 267 " pdb=" C LEU R 267 " ideal model delta sigma weight residual 112.23 100.72 11.51 1.26e+00 6.30e-01 8.34e+01 angle pdb=" N TRP R 268 " pdb=" CA TRP R 268 " pdb=" C TRP R 268 " ideal model delta sigma weight residual 111.36 102.25 9.11 1.09e+00 8.42e-01 6.98e+01 angle pdb=" N ASP R 104 " pdb=" CA ASP R 104 " pdb=" C ASP R 104 " ideal model delta sigma weight residual 108.24 95.67 12.57 1.81e+00 3.05e-01 4.82e+01 angle pdb=" N LEU R 103 " pdb=" CA LEU R 103 " pdb=" C LEU R 103 " ideal model delta sigma weight residual 110.53 102.11 8.42 1.29e+00 6.01e-01 4.26e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4836 17.93 - 35.85: 451 35.85 - 53.78: 103 53.78 - 71.70: 18 71.70 - 89.63: 7 Dihedral angle restraints: 5415 sinusoidal: 2082 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS B 19 " pdb=" CB CYS B 19 " ideal model delta sinusoidal sigma weight residual 93.00 163.18 -70.18 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CD ARG B 23 " pdb=" NE ARG B 23 " pdb=" CZ ARG B 23 " pdb=" NH1 ARG B 23 " ideal model delta sinusoidal sigma weight residual 0.00 -59.47 59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS B 7 " pdb=" CB CYS B 7 " ideal model delta sinusoidal sigma weight residual 93.00 54.62 38.38 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 5412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1286 0.077 - 0.154: 129 0.154 - 0.230: 2 0.230 - 0.307: 2 0.307 - 0.384: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA THR R 121 " pdb=" N THR R 121 " pdb=" C THR R 121 " pdb=" CB THR R 121 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PHE R 105 " pdb=" N PHE R 105 " pdb=" C PHE R 105 " pdb=" CB PHE R 105 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR B 14 " pdb=" N THR B 14 " pdb=" C THR B 14 " pdb=" CB THR B 14 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1419 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.947 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG B 23 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 102 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ALA R 102 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA R 102 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 103 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 266 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C THR R 266 " 0.041 2.00e-02 2.50e+03 pdb=" O THR R 266 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU R 267 " -0.014 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 402 2.72 - 3.27: 9102 3.27 - 3.81: 14279 3.81 - 4.35: 17413 4.35 - 4.90: 30077 Nonbonded interactions: 71273 Sorted by model distance: nonbonded pdb=" OG SER T 331 " pdb=" OD1 ASP T 333 " model vdw 2.175 3.040 nonbonded pdb=" O TYR R 284 " pdb=" OG1 THR R 288 " model vdw 2.212 3.040 nonbonded pdb=" OG SER T 97 " pdb=" OD2 ASP T 118 " model vdw 2.220 3.040 nonbonded pdb=" OG SER T 161 " pdb=" OD1 ASP T 163 " model vdw 2.222 3.040 nonbonded pdb=" O ILE T 58 " pdb=" OG SER T 316 " model vdw 2.228 3.040 ... (remaining 71268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.004 0.102 9181 Z= 0.266 Angle : 0.670 13.743 12457 Z= 0.398 Chirality : 0.047 0.384 1422 Planarity : 0.011 0.424 1569 Dihedral : 14.733 89.630 3248 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 1.55 % Allowed : 0.62 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.26), residues: 1130 helix: 0.51 (0.28), residues: 360 sheet: -0.94 (0.32), residues: 275 loop : -0.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.024 0.001 TYR T 59 PHE 0.012 0.001 PHE T 234 TRP 0.016 0.001 TRP R 200 HIS 0.002 0.001 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9176) covalent geometry : angle 0.66921 (12447) SS BOND : bond 0.00349 ( 5) SS BOND : angle 1.40241 ( 10) hydrogen bonds : bond 0.20043 ( 371) hydrogen bonds : angle 7.52495 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ILE cc_start: 0.7538 (mm) cc_final: 0.7240 (mm) REVERT: G 27 ARG cc_start: 0.6762 (mpt180) cc_final: 0.6488 (mmm-85) REVERT: G 38 MET cc_start: 0.8145 (pmm) cc_final: 0.7356 (pmm) REVERT: I 24 ARG cc_start: 0.6768 (mtp-110) cc_final: 0.6416 (mtm110) REVERT: I 26 ASP cc_start: 0.6893 (m-30) cc_final: 0.6690 (m-30) REVERT: I 33 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6760 (mm-30) REVERT: I 189 HIS cc_start: 0.7135 (t70) cc_final: 0.6864 (t-90) REVERT: I 192 PHE cc_start: 0.8205 (t80) cc_final: 0.7902 (t80) REVERT: I 217 GLU cc_start: 0.6925 (pt0) cc_final: 0.6616 (pt0) REVERT: I 252 ASP cc_start: 0.7250 (p0) cc_final: 0.6952 (t0) REVERT: I 270 ASN cc_start: 0.8669 (m-40) cc_final: 0.8413 (m-40) REVERT: I 271 LYS cc_start: 0.8802 (mttp) cc_final: 0.8592 (mtpt) REVERT: I 310 ASP cc_start: 0.7701 (m-30) cc_final: 0.7407 (m-30) REVERT: I 319 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6100 (tp30) REVERT: I 346 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6739 (ttmt) REVERT: R 41 MET cc_start: 0.4707 (mtt) cc_final: 0.4237 (mmt) REVERT: S 202 ARG cc_start: 0.8294 (ptp90) cc_final: 0.8024 (ptp90) REVERT: S 223 ASP cc_start: 0.7125 (m-30) cc_final: 0.6648 (m-30) REVERT: T 119 ASN cc_start: 0.9041 (m-40) cc_final: 0.8805 (m-40) REVERT: T 130 GLU cc_start: 0.7030 (pm20) cc_final: 0.6792 (pm20) REVERT: T 155 ASN cc_start: 0.7844 (t0) cc_final: 0.7198 (t0) REVERT: T 217 MET cc_start: 0.5639 (ptm) cc_final: 0.5315 (ttt) REVERT: T 229 ILE cc_start: 0.8754 (mt) cc_final: 0.8483 (mt) REVERT: T 308 LEU cc_start: 0.8762 (mp) cc_final: 0.8546 (mp) outliers start: 15 outliers final: 1 residues processed: 272 average time/residue: 0.0990 time to fit residues: 35.6340 Evaluate side-chains 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN I 305 GLN R 82 ASN R 106 HIS R 232 GLN R 262 ASN R 263 HIS R 305 ASN S 113 GLN T 110 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.203736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135857 restraints weight = 10700.311| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.46 r_work: 0.3291 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9181 Z= 0.172 Angle : 0.628 8.605 12457 Z= 0.326 Chirality : 0.045 0.191 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.886 61.240 1250 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.75 % Allowed : 10.82 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.25), residues: 1130 helix: 0.67 (0.27), residues: 359 sheet: -0.65 (0.31), residues: 281 loop : -0.97 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 5 TYR 0.016 0.002 TYR B 11 PHE 0.019 0.002 PHE R 195 TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9176) covalent geometry : angle 0.62239 (12447) SS BOND : bond 0.00426 ( 5) SS BOND : angle 3.08202 ( 10) hydrogen bonds : bond 0.04537 ( 371) hydrogen bonds : angle 5.09402 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ILE cc_start: 0.7410 (mm) cc_final: 0.7086 (mm) REVERT: G 27 ARG cc_start: 0.6964 (mpt180) cc_final: 0.6506 (mmm-85) REVERT: G 38 MET cc_start: 0.8233 (pmm) cc_final: 0.7576 (pmm) REVERT: I 24 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6889 (mtm110) REVERT: I 26 ASP cc_start: 0.7283 (m-30) cc_final: 0.7041 (m-30) REVERT: I 217 GLU cc_start: 0.7541 (pt0) cc_final: 0.7290 (pt0) REVERT: I 346 LYS cc_start: 0.7535 (ttmt) cc_final: 0.7236 (ttmt) REVERT: R 41 MET cc_start: 0.5262 (mtt) cc_final: 0.4528 (mmt) REVERT: R 130 PHE cc_start: 0.8474 (m-80) cc_final: 0.7673 (m-80) REVERT: R 262 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (m110) REVERT: S 160 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7902 (ttp80) REVERT: S 202 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7823 (ptp90) REVERT: S 219 LEU cc_start: 0.8361 (mm) cc_final: 0.7934 (tp) REVERT: T 130 GLU cc_start: 0.7397 (pm20) cc_final: 0.7093 (pm20) REVERT: T 155 ASN cc_start: 0.8263 (t0) cc_final: 0.7625 (t0) REVERT: T 229 ILE cc_start: 0.8957 (mt) cc_final: 0.8712 (mt) REVERT: T 280 LYS cc_start: 0.9010 (tptm) cc_final: 0.8792 (tttp) REVERT: T 308 LEU cc_start: 0.9009 (mp) cc_final: 0.8751 (mp) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.0944 time to fit residues: 28.0711 Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 262 ASN Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 65 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 196 HIS I 270 ASN ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN R 305 ASN S 113 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131591 restraints weight = 10647.326| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.39 r_work: 0.3305 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9181 Z= 0.140 Angle : 0.581 8.871 12457 Z= 0.301 Chirality : 0.044 0.200 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.780 57.214 1250 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.86 % Allowed : 14.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1130 helix: 0.99 (0.28), residues: 344 sheet: -0.61 (0.31), residues: 281 loop : -0.98 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 129 TYR 0.015 0.001 TYR B 17 PHE 0.020 0.001 PHE I 192 TRP 0.012 0.001 TRP S 47 HIS 0.008 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9176) covalent geometry : angle 0.57518 (12447) SS BOND : bond 0.01088 ( 5) SS BOND : angle 3.04271 ( 10) hydrogen bonds : bond 0.03944 ( 371) hydrogen bonds : angle 4.65495 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6556 (mm) cc_final: 0.6351 (mp) REVERT: G 27 ARG cc_start: 0.7015 (mpt180) cc_final: 0.6544 (mmm-85) REVERT: G 38 MET cc_start: 0.8257 (pmm) cc_final: 0.7624 (pmm) REVERT: I 18 MET cc_start: 0.7879 (mtt) cc_final: 0.7673 (ttm) REVERT: I 24 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6772 (mtm110) REVERT: I 26 ASP cc_start: 0.7233 (m-30) cc_final: 0.6989 (m-30) REVERT: I 217 GLU cc_start: 0.7522 (pt0) cc_final: 0.7252 (pt0) REVERT: I 319 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6823 (tp30) REVERT: I 346 LYS cc_start: 0.7495 (ttmt) cc_final: 0.7184 (ttmt) REVERT: R 41 MET cc_start: 0.5268 (mtt) cc_final: 0.4555 (mmt) REVERT: R 130 PHE cc_start: 0.8453 (m-10) cc_final: 0.7705 (m-80) REVERT: R 262 ASN cc_start: 0.8463 (t0) cc_final: 0.8258 (m110) REVERT: R 274 PHE cc_start: 0.7731 (m-80) cc_final: 0.7402 (m-10) REVERT: S 160 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7989 (ttp80) REVERT: S 202 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7864 (ptp90) REVERT: T 155 ASN cc_start: 0.8307 (t0) cc_final: 0.7657 (t0) REVERT: T 229 ILE cc_start: 0.8921 (mt) cc_final: 0.8681 (mt) REVERT: T 258 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: T 308 LEU cc_start: 0.9004 (mp) cc_final: 0.8731 (mp) outliers start: 18 outliers final: 11 residues processed: 211 average time/residue: 0.0861 time to fit residues: 24.7716 Evaluate side-chains 198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 258 ASP Chi-restraints excluded: chain T residue 259 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 262 ASN R 263 HIS R 301 ASN R 305 ASN S 113 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.203925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140001 restraints weight = 10757.722| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.35 r_work: 0.3306 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9181 Z= 0.124 Angle : 0.565 7.398 12457 Z= 0.293 Chirality : 0.043 0.162 1422 Planarity : 0.004 0.046 1569 Dihedral : 4.698 56.208 1250 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.27 % Allowed : 16.91 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.25), residues: 1130 helix: 1.13 (0.29), residues: 333 sheet: -0.59 (0.31), residues: 280 loop : -0.87 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 129 TYR 0.015 0.001 TYR B 17 PHE 0.032 0.001 PHE S 68 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9176) covalent geometry : angle 0.55986 (12447) SS BOND : bond 0.00307 ( 5) SS BOND : angle 2.61704 ( 10) hydrogen bonds : bond 0.03642 ( 371) hydrogen bonds : angle 4.43029 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6457 (mm) cc_final: 0.6191 (mp) REVERT: G 27 ARG cc_start: 0.7084 (mpt180) cc_final: 0.6727 (mpt180) REVERT: G 38 MET cc_start: 0.8241 (pmm) cc_final: 0.7621 (pmm) REVERT: I 24 ARG cc_start: 0.7406 (mtp-110) cc_final: 0.6866 (mtm110) REVERT: I 26 ASP cc_start: 0.7271 (m-30) cc_final: 0.7028 (m-30) REVERT: I 217 GLU cc_start: 0.7498 (pt0) cc_final: 0.7118 (pt0) REVERT: I 319 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6796 (tp30) REVERT: I 346 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7231 (ttmt) REVERT: R 41 MET cc_start: 0.5366 (mtt) cc_final: 0.4593 (mmt) REVERT: R 130 PHE cc_start: 0.8433 (m-10) cc_final: 0.7651 (m-80) REVERT: R 273 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6552 (ptmm) REVERT: R 274 PHE cc_start: 0.7789 (m-80) cc_final: 0.7298 (m-10) REVERT: S 93 MET cc_start: 0.7950 (tpt) cc_final: 0.7730 (tpt) REVERT: S 160 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8004 (ttp80) REVERT: S 202 ARG cc_start: 0.8247 (ptp90) cc_final: 0.8008 (ptp90) REVERT: T 15 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8841 (mtmm) REVERT: T 155 ASN cc_start: 0.8312 (t0) cc_final: 0.7685 (t0) REVERT: T 229 ILE cc_start: 0.8899 (mt) cc_final: 0.8662 (mt) REVERT: T 258 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: T 308 LEU cc_start: 0.9002 (mp) cc_final: 0.8739 (mp) outliers start: 22 outliers final: 8 residues processed: 204 average time/residue: 0.0780 time to fit residues: 22.2081 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 273 LYS Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 258 ASP Chi-restraints excluded: chain T residue 259 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 205 GLN ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.204161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138463 restraints weight = 10673.763| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.32 r_work: 0.3290 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9181 Z= 0.124 Angle : 0.560 7.583 12457 Z= 0.290 Chirality : 0.042 0.150 1422 Planarity : 0.004 0.043 1569 Dihedral : 4.485 54.907 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.27 % Allowed : 18.56 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1130 helix: 0.98 (0.28), residues: 350 sheet: -0.47 (0.32), residues: 278 loop : -1.00 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.013 0.001 TYR B 17 PHE 0.013 0.001 PHE R 283 TRP 0.009 0.001 TRP T 82 HIS 0.004 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9176) covalent geometry : angle 0.55711 (12447) SS BOND : bond 0.00486 ( 5) SS BOND : angle 2.18861 ( 10) hydrogen bonds : bond 0.03459 ( 371) hydrogen bonds : angle 4.34580 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6560 (mm) cc_final: 0.6316 (mp) REVERT: G 38 MET cc_start: 0.8171 (pmm) cc_final: 0.7701 (pmm) REVERT: I 24 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.6898 (mtm110) REVERT: I 26 ASP cc_start: 0.7319 (m-30) cc_final: 0.7055 (m-30) REVERT: I 53 MET cc_start: 0.8148 (mtt) cc_final: 0.7703 (mtt) REVERT: I 217 GLU cc_start: 0.7585 (pt0) cc_final: 0.7185 (pt0) REVERT: I 346 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7237 (ttmt) REVERT: R 41 MET cc_start: 0.5370 (mtt) cc_final: 0.4578 (mmt) REVERT: R 130 PHE cc_start: 0.8392 (m-10) cc_final: 0.7684 (m-80) REVERT: R 274 PHE cc_start: 0.7790 (m-80) cc_final: 0.7555 (m-10) REVERT: S 160 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7947 (ttp80) REVERT: S 202 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7981 (ptp90) REVERT: T 15 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8820 (mtmm) REVERT: T 155 ASN cc_start: 0.8327 (t0) cc_final: 0.7729 (t0) REVERT: T 229 ILE cc_start: 0.8929 (mt) cc_final: 0.8711 (mt) REVERT: T 258 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6736 (m-30) outliers start: 22 outliers final: 14 residues processed: 194 average time/residue: 0.0989 time to fit residues: 26.3369 Evaluate side-chains 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 176 GLN Chi-restraints excluded: chain T residue 258 ASP Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 HIS R 299 HIS R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135010 restraints weight = 10666.235| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.33 r_work: 0.3245 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9181 Z= 0.194 Angle : 0.613 11.289 12457 Z= 0.315 Chirality : 0.044 0.159 1422 Planarity : 0.004 0.045 1569 Dihedral : 4.587 53.717 1248 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.58 % Allowed : 18.56 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1130 helix: 0.90 (0.28), residues: 350 sheet: -0.68 (0.30), residues: 298 loop : -1.03 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 129 TYR 0.014 0.002 TYR I 303 PHE 0.015 0.001 PHE T 199 TRP 0.013 0.001 TRP S 36 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9176) covalent geometry : angle 0.60801 (12447) SS BOND : bond 0.00861 ( 5) SS BOND : angle 2.74080 ( 10) hydrogen bonds : bond 0.03733 ( 371) hydrogen bonds : angle 4.45692 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6818 (mm) cc_final: 0.6586 (mp) REVERT: G 38 MET cc_start: 0.8328 (pmm) cc_final: 0.7755 (pmm) REVERT: I 24 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.7088 (mtm110) REVERT: I 217 GLU cc_start: 0.7640 (pt0) cc_final: 0.7255 (pt0) REVERT: I 316 ASP cc_start: 0.6367 (t0) cc_final: 0.6018 (t0) REVERT: I 346 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7293 (ttmt) REVERT: R 41 MET cc_start: 0.5412 (mtt) cc_final: 0.4567 (mmm) REVERT: R 105 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7967 (p90) REVERT: R 130 PHE cc_start: 0.8466 (m-10) cc_final: 0.7742 (m-80) REVERT: R 274 PHE cc_start: 0.7651 (m-80) cc_final: 0.7436 (m-10) REVERT: S 160 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7961 (ttp80) REVERT: S 202 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7914 (ptp90) REVERT: T 15 LYS cc_start: 0.9057 (mtmm) cc_final: 0.8742 (mtmm) REVERT: T 155 ASN cc_start: 0.8522 (t0) cc_final: 0.8012 (t0) outliers start: 25 outliers final: 13 residues processed: 198 average time/residue: 0.0971 time to fit residues: 26.2386 Evaluate side-chains 195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS R 301 ASN R 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.203424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129954 restraints weight = 10680.335| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.90 r_work: 0.3318 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9181 Z= 0.122 Angle : 0.564 7.315 12457 Z= 0.292 Chirality : 0.042 0.154 1422 Planarity : 0.004 0.044 1569 Dihedral : 4.479 52.736 1248 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.16 % Allowed : 19.90 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1130 helix: 0.93 (0.28), residues: 350 sheet: -0.52 (0.31), residues: 282 loop : -0.93 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.011 0.001 TYR S 59 PHE 0.013 0.001 PHE R 283 TRP 0.016 0.001 TRP R 279 HIS 0.003 0.000 HIS R 152 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9176) covalent geometry : angle 0.56191 (12447) SS BOND : bond 0.00288 ( 5) SS BOND : angle 1.67090 ( 10) hydrogen bonds : bond 0.03430 ( 371) hydrogen bonds : angle 4.34657 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8224 (pmm) cc_final: 0.7708 (pmm) REVERT: I 24 ARG cc_start: 0.7311 (mtp-110) cc_final: 0.6826 (mtm110) REVERT: I 217 GLU cc_start: 0.7526 (pt0) cc_final: 0.7120 (pt0) REVERT: I 346 LYS cc_start: 0.7340 (ttmt) cc_final: 0.7049 (ttmt) REVERT: R 41 MET cc_start: 0.5140 (mtt) cc_final: 0.4355 (mmm) REVERT: R 130 PHE cc_start: 0.8353 (m-10) cc_final: 0.7612 (m-80) REVERT: R 305 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7609 (t160) REVERT: S 160 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7938 (ttp80) REVERT: S 202 ARG cc_start: 0.8163 (ptp90) cc_final: 0.7828 (ptp90) REVERT: T 155 ASN cc_start: 0.8369 (t0) cc_final: 0.7878 (t0) REVERT: T 264 TYR cc_start: 0.9128 (m-80) cc_final: 0.8572 (m-80) outliers start: 21 outliers final: 10 residues processed: 205 average time/residue: 0.0972 time to fit residues: 27.3082 Evaluate side-chains 197 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 259 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 32 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS R 299 HIS R 301 ASN R 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.203734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130488 restraints weight = 10633.531| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.90 r_work: 0.3322 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.125 Angle : 0.593 8.182 12457 Z= 0.300 Chirality : 0.042 0.151 1422 Planarity : 0.004 0.042 1569 Dihedral : 4.421 52.782 1248 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 20.31 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1130 helix: 0.95 (0.28), residues: 347 sheet: -0.51 (0.31), residues: 283 loop : -0.92 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 129 TYR 0.010 0.001 TYR S 59 PHE 0.015 0.001 PHE R 283 TRP 0.013 0.001 TRP R 107 HIS 0.002 0.001 HIS R 152 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9176) covalent geometry : angle 0.59240 (12447) SS BOND : bond 0.00287 ( 5) SS BOND : angle 1.39316 ( 10) hydrogen bonds : bond 0.03405 ( 371) hydrogen bonds : angle 4.30319 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8232 (pmm) cc_final: 0.7791 (pmm) REVERT: I 24 ARG cc_start: 0.7297 (mtp-110) cc_final: 0.6810 (mtm110) REVERT: I 26 ASP cc_start: 0.7156 (m-30) cc_final: 0.6923 (m-30) REVERT: I 217 GLU cc_start: 0.7501 (pt0) cc_final: 0.7079 (pt0) REVERT: I 299 GLU cc_start: 0.7784 (pm20) cc_final: 0.7433 (pm20) REVERT: I 346 LYS cc_start: 0.7305 (ttmt) cc_final: 0.7005 (ttmt) REVERT: R 41 MET cc_start: 0.5153 (mtt) cc_final: 0.4357 (mmm) REVERT: R 130 PHE cc_start: 0.8268 (m-10) cc_final: 0.7511 (m-80) REVERT: R 274 PHE cc_start: 0.7659 (m-10) cc_final: 0.7309 (m-10) REVERT: S 160 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7979 (ttp80) REVERT: S 202 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7808 (ptp90) REVERT: T 129 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8066 (ttt90) REVERT: T 155 ASN cc_start: 0.8349 (t0) cc_final: 0.7878 (t0) REVERT: T 264 TYR cc_start: 0.9110 (m-80) cc_final: 0.8625 (m-80) outliers start: 17 outliers final: 11 residues processed: 196 average time/residue: 0.1021 time to fit residues: 27.2638 Evaluate side-chains 194 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 GLN R 263 HIS R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134747 restraints weight = 10599.672| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.47 r_work: 0.3207 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9181 Z= 0.159 Angle : 0.618 8.659 12457 Z= 0.314 Chirality : 0.043 0.154 1422 Planarity : 0.004 0.043 1569 Dihedral : 4.483 53.305 1248 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.65 % Allowed : 21.03 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1130 helix: 0.95 (0.28), residues: 352 sheet: -0.51 (0.31), residues: 293 loop : -0.98 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.019 0.001 TYR I 303 PHE 0.016 0.001 PHE R 283 TRP 0.012 0.001 TRP T 339 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9176) covalent geometry : angle 0.61710 (12447) SS BOND : bond 0.00343 ( 5) SS BOND : angle 1.29340 ( 10) hydrogen bonds : bond 0.03543 ( 371) hydrogen bonds : angle 4.38512 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8253 (pmm) cc_final: 0.7810 (pmm) REVERT: I 24 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7117 (mtm110) REVERT: I 26 ASP cc_start: 0.7301 (m-30) cc_final: 0.7066 (m-30) REVERT: I 217 GLU cc_start: 0.7728 (pt0) cc_final: 0.7349 (pt0) REVERT: I 299 GLU cc_start: 0.7811 (pm20) cc_final: 0.7478 (pm20) REVERT: I 346 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7323 (ttmt) REVERT: R 41 MET cc_start: 0.5178 (mtt) cc_final: 0.4368 (mmm) REVERT: R 130 PHE cc_start: 0.8441 (m-10) cc_final: 0.7747 (m-80) REVERT: S 160 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8004 (ttp80) REVERT: T 264 TYR cc_start: 0.9109 (m-80) cc_final: 0.8850 (m-80) outliers start: 16 outliers final: 12 residues processed: 194 average time/residue: 0.1075 time to fit residues: 28.1504 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 HIS R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.202586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136571 restraints weight = 10597.150| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.25 r_work: 0.3263 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.147 Angle : 0.619 9.134 12457 Z= 0.314 Chirality : 0.043 0.153 1422 Planarity : 0.004 0.042 1569 Dihedral : 4.481 53.188 1248 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.44 % Allowed : 21.65 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1130 helix: 0.97 (0.28), residues: 352 sheet: -0.46 (0.31), residues: 276 loop : -1.07 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 129 TYR 0.017 0.001 TYR I 303 PHE 0.017 0.001 PHE R 283 TRP 0.013 0.001 TRP R 107 HIS 0.002 0.001 HIS T 91 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9176) covalent geometry : angle 0.61848 (12447) SS BOND : bond 0.00447 ( 5) SS BOND : angle 1.34433 ( 10) hydrogen bonds : bond 0.03486 ( 371) hydrogen bonds : angle 4.37223 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8269 (pmm) cc_final: 0.7878 (pmm) REVERT: I 24 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7100 (mtm110) REVERT: I 26 ASP cc_start: 0.7209 (m-30) cc_final: 0.6964 (m-30) REVERT: I 217 GLU cc_start: 0.7671 (pt0) cc_final: 0.7276 (pt0) REVERT: I 299 GLU cc_start: 0.7726 (pm20) cc_final: 0.7387 (pm20) REVERT: I 346 LYS cc_start: 0.7544 (ttmt) cc_final: 0.7233 (ttmt) REVERT: R 41 MET cc_start: 0.5113 (mtt) cc_final: 0.4277 (mmm) REVERT: R 130 PHE cc_start: 0.8403 (m-10) cc_final: 0.7702 (m-80) REVERT: R 314 ARG cc_start: 0.6703 (tpt90) cc_final: 0.6013 (mmt-90) REVERT: S 140 MET cc_start: 0.7932 (mtt) cc_final: 0.7692 (mtt) REVERT: S 160 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8043 (ttp80) REVERT: S 202 ARG cc_start: 0.8220 (ptp-170) cc_final: 0.7881 (ptp90) REVERT: T 262 MET cc_start: 0.7829 (ttt) cc_final: 0.7598 (ptm) outliers start: 14 outliers final: 12 residues processed: 191 average time/residue: 0.1113 time to fit residues: 28.7193 Evaluate side-chains 193 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 186 ASP Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 348 ASN R 152 HIS R 263 HIS R 301 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.202784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136466 restraints weight = 10440.546| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.34 r_work: 0.3268 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9181 Z= 0.146 Angle : 0.626 8.592 12457 Z= 0.315 Chirality : 0.043 0.156 1422 Planarity : 0.004 0.042 1569 Dihedral : 4.454 53.153 1248 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.55 % Allowed : 21.86 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1130 helix: 0.98 (0.28), residues: 348 sheet: -0.44 (0.31), residues: 276 loop : -1.01 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.017 0.001 TYR I 303 PHE 0.028 0.001 PHE R 105 TRP 0.013 0.001 TRP R 107 HIS 0.002 0.001 HIS T 91 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9176) covalent geometry : angle 0.62487 (12447) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.25176 ( 10) hydrogen bonds : bond 0.03490 ( 371) hydrogen bonds : angle 4.36321 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.18 seconds wall clock time: 48 minutes 31.76 seconds (2911.76 seconds total)