Starting phenix.real_space_refine on Thu Feb 13 13:49:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj4_33871/02_2025/7yj4_33871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj4_33871/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yj4_33871/02_2025/7yj4_33871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj4_33871/02_2025/7yj4_33871.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj4_33871/02_2025/7yj4_33871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj4_33871/02_2025/7yj4_33871.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.20, per 1000 atoms: 0.58 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: 2.21 Conformation dependent library (CDL) restraints added in 965.8 milliseconds 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: 1.12 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: 2.63 Time building geometry restraints manager: 2.55 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: 0.970 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- 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 9176 Z= 0.265 Angle : 0.669 13.743 12447 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 : 9.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (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 TRP 0.016 0.001 TRP R 200 HIS 0.002 0.001 HIS R 106 PHE 0.012 0.001 PHE T 234 TYR 0.024 0.001 TYR T 59 ARG 0.009 0.000 ARG S 160 *********************** 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 : 0.988 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: 0.2508 time to fit residues: 89.4830 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 : 1.060 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.204536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132400 restraints weight = 10604.755| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.36 r_work: 0.3313 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9176 Z= 0.247 Angle : 0.616 8.334 12447 Z= 0.322 Chirality : 0.044 0.184 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.841 62.231 1250 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.65 % Allowed : 10.62 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1130 helix: 0.68 (0.27), residues: 360 sheet: -0.61 (0.32), residues: 274 loop : -0.95 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 279 HIS 0.004 0.001 HIS R 263 PHE 0.017 0.001 PHE S 68 TYR 0.015 0.002 TYR R 289 ARG 0.006 0.001 ARG B 5 *********************** 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 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ILE cc_start: 0.7414 (mm) cc_final: 0.7128 (mm) REVERT: G 27 ARG cc_start: 0.6908 (mpt180) cc_final: 0.6401 (mmm-85) REVERT: G 38 MET cc_start: 0.8220 (pmm) cc_final: 0.7561 (pmm) REVERT: I 24 ARG cc_start: 0.7321 (mtp-110) cc_final: 0.6808 (mtm110) REVERT: I 26 ASP cc_start: 0.7241 (m-30) cc_final: 0.6998 (m-30) REVERT: I 217 GLU cc_start: 0.7489 (pt0) cc_final: 0.7235 (pt0) REVERT: I 346 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7199 (ttmt) REVERT: R 41 MET cc_start: 0.5259 (mtt) cc_final: 0.4527 (mmt) REVERT: R 262 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7908 (m110) REVERT: S 160 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7919 (ttp80) REVERT: S 202 ARG cc_start: 0.8222 (ptp90) cc_final: 0.7811 (ptp90) REVERT: S 219 LEU cc_start: 0.8349 (mm) cc_final: 0.7930 (tp) REVERT: S 223 ASP cc_start: 0.7129 (m-30) cc_final: 0.6390 (m-30) REVERT: T 130 GLU cc_start: 0.7393 (pm20) cc_final: 0.7091 (pm20) REVERT: T 155 ASN cc_start: 0.8209 (t0) cc_final: 0.7575 (t0) REVERT: T 197 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8290 (tpp80) REVERT: T 229 ILE cc_start: 0.8941 (mt) cc_final: 0.8676 (mt) REVERT: T 308 LEU cc_start: 0.8985 (mp) cc_final: 0.8730 (mp) outliers start: 16 outliers final: 8 residues processed: 211 average time/residue: 0.2353 time to fit residues: 66.6844 Evaluate side-chains 188 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 TRP Chi-restraints excluded: chain R residue 262 ASN Chi-restraints excluded: chain R residue 276 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 205 GLN ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN R 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.204834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132069 restraints weight = 10727.143| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.40 r_work: 0.3297 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9176 Z= 0.202 Angle : 0.572 8.755 12447 Z= 0.296 Chirality : 0.044 0.212 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.750 57.530 1250 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.06 % Allowed : 12.89 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1130 helix: 0.92 (0.28), residues: 350 sheet: -0.57 (0.32), residues: 277 loop : -0.99 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.010 0.001 HIS R 263 PHE 0.019 0.001 PHE S 68 TYR 0.016 0.001 TYR B 17 ARG 0.006 0.000 ARG T 129 *********************** 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 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 ARG cc_start: 0.6936 (mpt180) cc_final: 0.6504 (mmm-85) REVERT: G 38 MET cc_start: 0.8255 (pmm) cc_final: 0.7616 (pmm) REVERT: I 24 ARG cc_start: 0.7338 (mtp-110) cc_final: 0.6767 (mtm110) REVERT: I 26 ASP cc_start: 0.7256 (m-30) cc_final: 0.7014 (m-30) REVERT: I 217 GLU cc_start: 0.7505 (pt0) cc_final: 0.7246 (pt0) REVERT: I 346 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7184 (ttmt) REVERT: R 41 MET cc_start: 0.5202 (mtt) cc_final: 0.4474 (mmt) REVERT: R 130 PHE cc_start: 0.8455 (m-10) cc_final: 0.7706 (m-80) REVERT: R 274 PHE cc_start: 0.7723 (m-80) cc_final: 0.7293 (m-10) REVERT: S 160 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7939 (ttp80) REVERT: S 202 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7873 (ptp90) REVERT: S 219 LEU cc_start: 0.8444 (mm) cc_final: 0.8037 (tp) REVERT: S 223 ASP cc_start: 0.7103 (m-30) cc_final: 0.6367 (m-30) REVERT: T 155 ASN cc_start: 0.8299 (t0) cc_final: 0.7645 (t0) REVERT: T 197 ARG cc_start: 0.8464 (tpp-160) cc_final: 0.8243 (tpp-160) REVERT: T 229 ILE cc_start: 0.8914 (mt) cc_final: 0.8673 (mt) REVERT: T 308 LEU cc_start: 0.8998 (mp) cc_final: 0.8737 (mp) outliers start: 20 outliers final: 12 residues processed: 205 average time/residue: 0.2330 time to fit residues: 64.8302 Evaluate side-chains 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 41 CYS 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 259 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** S 113 GLN ** T 32 GLN ** 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 = 0.4292 r_free = 0.4292 target = 0.203067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131185 restraints weight = 10583.504| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.39 r_work: 0.3266 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9176 Z= 0.229 Angle : 0.576 7.333 12447 Z= 0.299 Chirality : 0.043 0.151 1422 Planarity : 0.004 0.046 1569 Dihedral : 4.757 56.228 1250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.47 % Allowed : 16.29 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1130 helix: 1.11 (0.28), residues: 338 sheet: -0.61 (0.31), residues: 280 loop : -0.96 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 107 HIS 0.006 0.001 HIS R 263 PHE 0.035 0.001 PHE S 68 TYR 0.016 0.002 TYR B 17 ARG 0.006 0.000 ARG T 129 *********************** 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 213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8266 (pmm) cc_final: 0.7658 (pmm) REVERT: I 24 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.6746 (mtm110) REVERT: I 26 ASP cc_start: 0.7216 (m-30) cc_final: 0.6955 (m-30) REVERT: I 217 GLU cc_start: 0.7518 (pt0) cc_final: 0.7118 (pt0) REVERT: I 346 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7109 (ttmt) REVERT: R 41 MET cc_start: 0.5435 (mtt) cc_final: 0.4623 (mmt) REVERT: R 274 PHE cc_start: 0.7874 (m-80) cc_final: 0.7343 (m-10) REVERT: R 301 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6841 (m110) REVERT: S 93 MET cc_start: 0.7965 (tpt) cc_final: 0.7706 (tpt) REVERT: S 160 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7873 (ttp80) REVERT: S 202 ARG cc_start: 0.8176 (ptp90) cc_final: 0.7879 (ptp90) REVERT: S 223 ASP cc_start: 0.7133 (m-30) cc_final: 0.6587 (m-30) REVERT: T 15 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8852 (mtmm) REVERT: T 155 ASN cc_start: 0.8304 (t0) cc_final: 0.7683 (t0) REVERT: T 229 ILE cc_start: 0.8922 (mt) cc_final: 0.8691 (mt) REVERT: T 308 LEU cc_start: 0.9011 (mp) cc_final: 0.8742 (mp) outliers start: 24 outliers final: 12 residues processed: 200 average time/residue: 0.2134 time to fit residues: 58.4108 Evaluate side-chains 199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 301 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 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 259 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.199561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132695 restraints weight = 10617.307| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.30 r_work: 0.3217 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9176 Z= 0.367 Angle : 0.627 8.449 12447 Z= 0.329 Chirality : 0.045 0.166 1422 Planarity : 0.004 0.049 1569 Dihedral : 4.845 54.575 1248 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.78 % Allowed : 18.45 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1130 helix: 0.94 (0.28), residues: 344 sheet: -0.79 (0.30), residues: 287 loop : -1.09 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 107 HIS 0.006 0.001 HIS R 263 PHE 0.016 0.002 PHE R 109 TYR 0.015 0.002 TYR S 175 ARG 0.007 0.001 ARG T 129 *********************** 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 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8415 (pmm) cc_final: 0.8022 (pmm) REVERT: G 50 LEU cc_start: 0.7895 (mt) cc_final: 0.7679 (mt) REVERT: I 24 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7081 (mtm110) REVERT: I 26 ASP cc_start: 0.7273 (m-30) cc_final: 0.7018 (m-30) REVERT: I 209 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7734 (mtp-110) REVERT: I 217 GLU cc_start: 0.7673 (pt0) cc_final: 0.7292 (pt0) REVERT: I 316 ASP cc_start: 0.6388 (t0) cc_final: 0.6046 (t0) REVERT: I 346 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7272 (ttmt) REVERT: R 41 MET cc_start: 0.5457 (mtt) cc_final: 0.4602 (mmm) REVERT: R 274 PHE cc_start: 0.7755 (m-80) cc_final: 0.7519 (m-10) REVERT: S 160 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7879 (ttp80) REVERT: S 202 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7866 (ptp90) REVERT: S 223 ASP cc_start: 0.7269 (m-30) cc_final: 0.6733 (m-30) REVERT: T 155 ASN cc_start: 0.8488 (t0) cc_final: 0.8033 (t0) REVERT: T 308 LEU cc_start: 0.9038 (mp) cc_final: 0.8765 (mp) outliers start: 27 outliers final: 12 residues processed: 208 average time/residue: 0.2367 time to fit residues: 66.2712 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 290 VAL 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 133 VAL Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 259 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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 = 0.4273 r_free = 0.4273 target = 0.201549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127490 restraints weight = 10472.900| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.90 r_work: 0.3268 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9176 Z= 0.220 Angle : 0.579 7.317 12447 Z= 0.301 Chirality : 0.043 0.142 1422 Planarity : 0.004 0.049 1569 Dihedral : 4.630 53.748 1248 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.96 % Allowed : 18.97 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1130 helix: 0.87 (0.28), residues: 357 sheet: -0.61 (0.31), residues: 284 loop : -1.01 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.017 0.001 PHE R 109 TYR 0.014 0.002 TYR I 303 ARG 0.007 0.000 ARG T 129 *********************** 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 213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8332 (pmm) cc_final: 0.7744 (pmm) REVERT: I 24 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.6921 (mtm110) REVERT: I 26 ASP cc_start: 0.7162 (m-30) cc_final: 0.6906 (m-30) REVERT: I 33 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7634 (mt-10) REVERT: I 217 GLU cc_start: 0.7574 (pt0) cc_final: 0.7161 (pt0) REVERT: I 319 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6581 (tp30) REVERT: I 346 LYS cc_start: 0.7371 (ttmt) cc_final: 0.7000 (ttmt) REVERT: R 41 MET cc_start: 0.5195 (mtt) cc_final: 0.4388 (mmm) REVERT: R 130 PHE cc_start: 0.8392 (m-10) cc_final: 0.7593 (m-80) REVERT: S 160 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7953 (ttp80) REVERT: S 202 ARG cc_start: 0.8173 (ptp90) cc_final: 0.7757 (ptp90) REVERT: S 223 ASP cc_start: 0.7294 (m-30) cc_final: 0.6721 (m-30) REVERT: T 15 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8919 (pttm) REVERT: T 258 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: T 264 TYR cc_start: 0.9187 (m-80) cc_final: 0.8567 (m-80) outliers start: 19 outliers final: 11 residues processed: 205 average time/residue: 0.2236 time to fit residues: 62.3098 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 : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain R residue 276 LEU 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 161 SER Chi-restraints excluded: chain T residue 258 ASP Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.0000 chunk 3 optimal weight: 0.1980 chunk 111 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.203132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134347 restraints weight = 10705.997| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.41 r_work: 0.3253 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9176 Z= 0.167 Angle : 0.566 7.480 12447 Z= 0.293 Chirality : 0.042 0.182 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.578 53.828 1248 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.96 % Allowed : 19.38 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1130 helix: 0.93 (0.28), residues: 349 sheet: -0.56 (0.31), residues: 282 loop : -0.99 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP R 107 HIS 0.003 0.000 HIS R 152 PHE 0.011 0.001 PHE S 68 TYR 0.012 0.001 TYR R 199 ARG 0.007 0.000 ARG T 129 *********************** 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 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8359 (pmm) cc_final: 0.7821 (pmm) REVERT: G 62 ARG cc_start: 0.7043 (mmp80) cc_final: 0.6842 (mmp80) REVERT: I 24 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.6998 (mtm110) REVERT: I 26 ASP cc_start: 0.7360 (m-30) cc_final: 0.7129 (m-30) REVERT: I 217 GLU cc_start: 0.7613 (pt0) cc_final: 0.7218 (pt0) REVERT: I 346 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7243 (ttmt) REVERT: R 41 MET cc_start: 0.5193 (mtt) cc_final: 0.4382 (mmm) REVERT: R 130 PHE cc_start: 0.8436 (m-10) cc_final: 0.7713 (m-80) REVERT: S 160 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7934 (ttp80) REVERT: S 202 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7843 (ptp90) REVERT: S 223 ASP cc_start: 0.7313 (m-30) cc_final: 0.6754 (m-30) REVERT: T 15 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8931 (pttm) REVERT: T 220 GLN cc_start: 0.8242 (mt0) cc_final: 0.7996 (mt0) REVERT: T 264 TYR cc_start: 0.9113 (m-80) cc_final: 0.8575 (m-80) outliers start: 19 outliers final: 10 residues processed: 203 average time/residue: 0.2131 time to fit residues: 58.9518 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 : 0.998 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 271 CYS Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ** 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 = 0.4293 r_free = 0.4293 target = 0.203668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137707 restraints weight = 10704.181| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.33 r_work: 0.3274 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9176 Z= 0.176 Angle : 0.573 7.545 12447 Z= 0.294 Chirality : 0.042 0.172 1422 Planarity : 0.004 0.046 1569 Dihedral : 4.483 54.615 1248 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.44 % Allowed : 20.52 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1130 helix: 0.97 (0.28), residues: 347 sheet: -0.46 (0.31), residues: 281 loop : -0.92 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 107 HIS 0.002 0.000 HIS T 91 PHE 0.026 0.001 PHE R 105 TYR 0.011 0.001 TYR S 59 ARG 0.008 0.000 ARG T 129 *********************** 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 199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8452 (pmm) cc_final: 0.7982 (pmm) REVERT: I 24 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.6993 (mtm110) REVERT: I 26 ASP cc_start: 0.7305 (m-30) cc_final: 0.7072 (m-30) REVERT: I 217 GLU cc_start: 0.7548 (pt0) cc_final: 0.7160 (pt0) REVERT: I 346 LYS cc_start: 0.7538 (ttmt) cc_final: 0.7218 (ttmt) REVERT: R 41 MET cc_start: 0.5160 (mtt) cc_final: 0.4361 (mmm) REVERT: R 130 PHE cc_start: 0.8391 (m-10) cc_final: 0.7667 (m-80) REVERT: S 160 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7981 (ttp80) REVERT: S 202 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7959 (ptp-170) REVERT: S 223 ASP cc_start: 0.7337 (m-30) cc_final: 0.6522 (m-30) REVERT: T 129 ARG cc_start: 0.8316 (ttt90) cc_final: 0.8099 (ttt90) REVERT: T 264 TYR cc_start: 0.9111 (m-80) cc_final: 0.8648 (m-80) outliers start: 14 outliers final: 9 residues processed: 194 average time/residue: 0.2229 time to fit residues: 58.6324 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 259 GLN Chi-restraints excluded: chain T residue 271 CYS 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 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 0.0170 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 GLN I 348 ASN R 152 HIS R 263 HIS ** 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 = 0.4296 r_free = 0.4296 target = 0.203799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130285 restraints weight = 10544.840| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.89 r_work: 0.3323 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9176 Z= 0.184 Angle : 0.587 8.039 12447 Z= 0.298 Chirality : 0.042 0.155 1422 Planarity : 0.004 0.047 1569 Dihedral : 4.420 54.683 1248 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 20.82 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1130 helix: 0.94 (0.28), residues: 355 sheet: -0.50 (0.31), residues: 283 loop : -0.82 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 107 HIS 0.002 0.001 HIS T 91 PHE 0.028 0.001 PHE R 105 TYR 0.018 0.001 TYR I 303 ARG 0.007 0.000 ARG T 129 *********************** 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: 17 poor density : 184 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8439 (pmm) cc_final: 0.7942 (pmm) REVERT: I 24 ARG cc_start: 0.7314 (mtp-110) cc_final: 0.6864 (mtm110) REVERT: I 26 ASP cc_start: 0.7157 (m-30) cc_final: 0.6920 (m-30) REVERT: I 217 GLU cc_start: 0.7464 (pt0) cc_final: 0.7047 (pt0) REVERT: I 346 LYS cc_start: 0.7311 (ttmt) cc_final: 0.7011 (ttmt) REVERT: R 41 MET cc_start: 0.5156 (mtt) cc_final: 0.4359 (mmm) REVERT: R 105 PHE cc_start: 0.7979 (p90) cc_final: 0.7735 (p90) REVERT: R 130 PHE cc_start: 0.8265 (m-10) cc_final: 0.7543 (m-80) REVERT: R 314 ARG cc_start: 0.6801 (tpt90) cc_final: 0.6059 (mmt-90) REVERT: S 160 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7961 (ttp80) REVERT: S 202 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7846 (ptp-170) REVERT: S 223 ASP cc_start: 0.7342 (m-30) cc_final: 0.6515 (m-30) REVERT: T 264 TYR cc_start: 0.9109 (m-80) cc_final: 0.8680 (m-80) outliers start: 17 outliers final: 10 residues processed: 193 average time/residue: 0.2323 time to fit residues: 60.2738 Evaluate side-chains 189 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 161 SER 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 39 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.202489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128458 restraints weight = 10660.773| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.93 r_work: 0.3301 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9176 Z= 0.233 Angle : 0.619 8.618 12447 Z= 0.315 Chirality : 0.043 0.215 1422 Planarity : 0.004 0.048 1569 Dihedral : 4.576 55.027 1248 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.34 % Allowed : 21.55 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1130 helix: 0.96 (0.28), residues: 349 sheet: -0.41 (0.31), residues: 275 loop : -0.99 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 279 HIS 0.003 0.001 HIS T 91 PHE 0.032 0.001 PHE R 105 TYR 0.018 0.001 TYR I 303 ARG 0.008 0.000 ARG T 129 ********************** 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 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6995 (mp) cc_final: 0.6709 (pp) REVERT: G 38 MET cc_start: 0.8474 (pmm) cc_final: 0.8013 (pmm) REVERT: I 24 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.6888 (mtm110) REVERT: I 26 ASP cc_start: 0.7121 (m-30) cc_final: 0.6881 (m-30) REVERT: I 217 GLU cc_start: 0.7556 (pt0) cc_final: 0.7137 (pt0) REVERT: I 299 GLU cc_start: 0.7647 (pm20) cc_final: 0.7225 (pm20) REVERT: I 346 LYS cc_start: 0.7355 (ttmt) cc_final: 0.7048 (ttmt) REVERT: R 41 MET cc_start: 0.5112 (mtt) cc_final: 0.4323 (mmm) REVERT: R 130 PHE cc_start: 0.8288 (m-10) cc_final: 0.7558 (m-80) REVERT: R 314 ARG cc_start: 0.6698 (tpt90) cc_final: 0.6005 (mmt-90) REVERT: S 93 MET cc_start: 0.7745 (tpt) cc_final: 0.7527 (tpt) REVERT: S 160 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8111 (ttp80) REVERT: S 202 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7826 (ptp-170) REVERT: S 223 ASP cc_start: 0.7353 (m-30) cc_final: 0.6518 (m-30) REVERT: T 220 GLN cc_start: 0.7882 (mt0) cc_final: 0.7479 (mt0) REVERT: T 264 TYR cc_start: 0.9116 (m-80) cc_final: 0.8822 (m-80) outliers start: 13 outliers final: 10 residues processed: 185 average time/residue: 0.2351 time to fit residues: 58.0234 Evaluate side-chains 188 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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 56 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 108 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 256 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131166 restraints weight = 10597.492| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.16 r_work: 0.3293 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9176 Z= 0.191 Angle : 0.613 8.380 12447 Z= 0.311 Chirality : 0.043 0.167 1422 Planarity : 0.004 0.046 1569 Dihedral : 4.583 54.866 1248 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.03 % Allowed : 22.16 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1130 helix: 1.02 (0.28), residues: 349 sheet: -0.39 (0.31), residues: 277 loop : -1.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 82 HIS 0.002 0.000 HIS T 91 PHE 0.029 0.001 PHE R 105 TYR 0.016 0.001 TYR I 303 ARG 0.005 0.000 ARG S 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.37 seconds wall clock time: 101 minutes 19.94 seconds (6079.94 seconds total)