Starting phenix.real_space_refine on Mon May 12 13:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj4_33871/05_2025/7yj4_33871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj4_33871/05_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_33871/05_2025/7yj4_33871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj4_33871/05_2025/7yj4_33871.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj4_33871/05_2025/7yj4_33871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj4_33871/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.22, 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 2.62 Time building geometry restraints manager: 2.54 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.440 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- 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 : 9.63 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 Details of bonding type rmsd hydrogen bonds : bond 0.20043 ( 371) hydrogen bonds : angle 7.52495 ( 1059) SS BOND : bond 0.00349 ( 5) SS BOND : angle 1.40241 ( 10) covalent geometry : bond 0.00407 ( 9176) covalent geometry : angle 0.66921 (12447) *********************** 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 : 1.108 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: 0.2426 time to fit residues: 86.7132 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 : 0.916 ------------------------------------------------------------------------------- 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 9181 Z= 0.169 Angle : 0.623 8.334 12457 Z= 0.325 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 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 371) hydrogen bonds : angle 5.14810 ( 1059) SS BOND : bond 0.00406 ( 5) SS BOND : angle 3.14265 ( 10) covalent geometry : bond 0.00378 ( 9176) covalent geometry : angle 0.61636 (12447) *********************** 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 : 1.110 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: 0.2273 time to fit residues: 64.7386 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 : 1.016 ------------------------------------------------------------------------------- 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 9181 Z= 0.136 Angle : 0.577 8.755 12457 Z= 0.299 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 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 371) hydrogen bonds : angle 4.67653 ( 1059) SS BOND : bond 0.00435 ( 5) SS BOND : angle 2.83170 ( 10) covalent geometry : bond 0.00307 ( 9176) covalent geometry : angle 0.57178 (12447) *********************** 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 : 0.926 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: 0.2135 time to fit residues: 59.3106 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 : 0.924 ------------------------------------------------------------------------------- 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 9181 Z= 0.151 Angle : 0.580 7.333 12457 Z= 0.301 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 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 371) hydrogen bonds : angle 4.48169 ( 1059) SS BOND : bond 0.00405 ( 5) SS BOND : angle 2.38606 ( 10) covalent geometry : bond 0.00350 ( 9176) covalent geometry : angle 0.57589 (12447) *********************** 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 : 0.938 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: 0.2070 time to fit residues: 56.7608 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 : 0.945 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.204034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139540 restraints weight = 10597.209| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.32 r_work: 0.3307 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9181 Z= 0.126 Angle : 0.558 7.216 12457 Z= 0.292 Chirality : 0.042 0.168 1422 Planarity : 0.004 0.045 1569 Dihedral : 4.537 55.026 1248 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.47 % Allowed : 17.73 % Favored : 79.79 % 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: -0.44 (0.25), residues: 1130 helix: 1.03 (0.28), residues: 344 sheet: -0.54 (0.31), residues: 276 loop : -1.02 (0.27), residues: 510 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 0.015 0.001 PHE S 68 TYR 0.013 0.001 TYR I 303 ARG 0.006 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 371) hydrogen bonds : angle 4.39858 ( 1059) SS BOND : bond 0.00554 ( 5) SS BOND : angle 2.69011 ( 10) covalent geometry : bond 0.00283 ( 9176) covalent geometry : angle 0.55339 (12447) *********************** 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 211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8280 (pmm) cc_final: 0.7713 (pmm) REVERT: I 24 ARG cc_start: 0.7380 (mtp-110) cc_final: 0.6869 (mtm110) REVERT: I 26 ASP cc_start: 0.7297 (m-30) cc_final: 0.7059 (m-30) REVERT: I 217 GLU cc_start: 0.7561 (pt0) cc_final: 0.7165 (pt0) REVERT: I 346 LYS cc_start: 0.7454 (ttmt) cc_final: 0.7167 (ttmt) REVERT: R 41 MET cc_start: 0.5390 (mtt) cc_final: 0.4595 (mmt) REVERT: R 130 PHE cc_start: 0.8409 (m-10) cc_final: 0.7655 (m-80) REVERT: R 274 PHE cc_start: 0.7648 (m-80) cc_final: 0.7439 (m-10) REVERT: S 3 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7658 (pp30) REVERT: S 160 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7899 (ttp80) REVERT: S 202 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7942 (ptp90) REVERT: S 223 ASP cc_start: 0.7242 (m-30) cc_final: 0.6737 (m-30) REVERT: T 15 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8864 (mtmm) REVERT: T 155 ASN cc_start: 0.8348 (t0) cc_final: 0.7758 (t0) REVERT: T 229 ILE cc_start: 0.8915 (mt) cc_final: 0.8697 (mt) outliers start: 24 outliers final: 10 residues processed: 202 average time/residue: 0.2199 time to fit residues: 60.9043 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 276 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 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: 0.7980 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.203419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138055 restraints weight = 10496.015| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.39 r_work: 0.3272 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9181 Z= 0.135 Angle : 0.562 7.529 12457 Z= 0.291 Chirality : 0.042 0.140 1422 Planarity : 0.004 0.044 1569 Dihedral : 4.479 54.669 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.37 % Allowed : 17.94 % Favored : 79.69 % 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: -0.42 (0.25), residues: 1130 helix: 0.94 (0.28), residues: 351 sheet: -0.56 (0.31), residues: 282 loop : -0.92 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.015 0.001 PHE R 109 TYR 0.014 0.001 TYR B 17 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 371) hydrogen bonds : angle 4.36935 ( 1059) SS BOND : bond 0.00612 ( 5) SS BOND : angle 0.81206 ( 10) covalent geometry : bond 0.00306 ( 9176) covalent geometry : angle 0.56143 (12447) *********************** 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 209 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8290 (pmm) cc_final: 0.7773 (pmm) REVERT: I 24 ARG cc_start: 0.7456 (mtp-110) cc_final: 0.6969 (mtm110) REVERT: I 53 MET cc_start: 0.8191 (mtt) cc_final: 0.7799 (mtt) REVERT: I 217 GLU cc_start: 0.7611 (pt0) cc_final: 0.7228 (pt0) REVERT: I 316 ASP cc_start: 0.6271 (t0) cc_final: 0.5927 (t0) REVERT: I 346 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7270 (ttmt) REVERT: R 41 MET cc_start: 0.5332 (mtt) cc_final: 0.4568 (mmt) REVERT: R 130 PHE cc_start: 0.8415 (m-10) cc_final: 0.7695 (m-80) REVERT: R 305 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7658 (t160) REVERT: S 160 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7967 (ttp80) REVERT: S 202 ARG cc_start: 0.8264 (ptp90) cc_final: 0.7956 (ptp90) REVERT: S 223 ASP cc_start: 0.7250 (m-30) cc_final: 0.6716 (m-30) REVERT: T 155 ASN cc_start: 0.8379 (t0) cc_final: 0.7830 (t0) REVERT: T 258 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: T 264 TYR cc_start: 0.9126 (m-80) cc_final: 0.8139 (m-80) outliers start: 23 outliers final: 15 residues processed: 198 average time/residue: 0.2234 time to fit residues: 60.3609 Evaluate side-chains 199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 113 LEU Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 305 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 161 SER Chi-restraints excluded: chain T residue 258 ASP 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 86 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.0040 chunk 3 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 57 ASN ** 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 = 0.4287 r_free = 0.4287 target = 0.202812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135268 restraints weight = 10728.537| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.24 r_work: 0.3273 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9181 Z= 0.143 Angle : 0.574 7.429 12457 Z= 0.297 Chirality : 0.043 0.179 1422 Planarity : 0.004 0.044 1569 Dihedral : 4.576 54.380 1248 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.58 % Allowed : 18.76 % 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: -0.43 (0.25), residues: 1130 helix: 0.97 (0.28), residues: 346 sheet: -0.57 (0.30), residues: 293 loop : -0.93 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.024 0.001 PHE I 335 TYR 0.015 0.001 TYR I 303 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 371) hydrogen bonds : angle 4.38023 ( 1059) SS BOND : bond 0.00377 ( 5) SS BOND : angle 2.83052 ( 10) covalent geometry : bond 0.00329 ( 9176) covalent geometry : angle 0.56836 (12447) *********************** 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 214 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8285 (pmm) cc_final: 0.7778 (pmm) REVERT: I 24 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.6939 (mtm110) REVERT: I 26 ASP cc_start: 0.7285 (m-30) cc_final: 0.7055 (m-30) REVERT: I 217 GLU cc_start: 0.7580 (pt0) cc_final: 0.7180 (pt0) REVERT: I 316 ASP cc_start: 0.6379 (t0) cc_final: 0.6107 (t0) REVERT: I 346 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7208 (ttmt) REVERT: R 41 MET cc_start: 0.5372 (mtt) cc_final: 0.4534 (mmm) REVERT: R 130 PHE cc_start: 0.8428 (m-10) cc_final: 0.7720 (m-80) REVERT: S 160 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7943 (ttp80) REVERT: S 202 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7899 (ptp90) REVERT: S 223 ASP cc_start: 0.7256 (m-30) cc_final: 0.6708 (m-30) REVERT: T 15 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8823 (pttm) REVERT: T 155 ASN cc_start: 0.8409 (t0) cc_final: 0.7884 (t0) REVERT: T 220 GLN cc_start: 0.8273 (mt0) cc_final: 0.8031 (mt0) REVERT: T 264 TYR cc_start: 0.9117 (m-80) cc_final: 0.8264 (m-80) outliers start: 25 outliers final: 13 residues processed: 202 average time/residue: 0.2155 time to fit residues: 59.0702 Evaluate side-chains 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 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 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 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.203974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137798 restraints weight = 10742.032| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.30 r_work: 0.3281 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9181 Z= 0.126 Angle : 0.596 7.524 12457 Z= 0.305 Chirality : 0.042 0.192 1422 Planarity : 0.004 0.043 1569 Dihedral : 4.533 54.561 1248 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.16 % Allowed : 19.18 % Favored : 78.66 % 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: -0.34 (0.25), residues: 1130 helix: 1.03 (0.28), residues: 343 sheet: -0.51 (0.31), residues: 291 loop : -0.86 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP R 107 HIS 0.003 0.001 HIS R 106 PHE 0.021 0.001 PHE I 335 TYR 0.013 0.001 TYR I 303 ARG 0.008 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 371) hydrogen bonds : angle 4.33322 ( 1059) SS BOND : bond 0.00632 ( 5) SS BOND : angle 3.28744 ( 10) covalent geometry : bond 0.00285 ( 9176) covalent geometry : angle 0.58921 (12447) *********************** 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 209 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8266 (pmm) cc_final: 0.7754 (pmm) REVERT: I 24 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.6944 (mtm110) REVERT: I 26 ASP cc_start: 0.7332 (m-30) cc_final: 0.7096 (m-30) REVERT: I 217 GLU cc_start: 0.7583 (pt0) cc_final: 0.7199 (pt0) REVERT: I 316 ASP cc_start: 0.6372 (t0) cc_final: 0.6085 (t0) REVERT: I 346 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7220 (ttmt) REVERT: R 41 MET cc_start: 0.5087 (mtt) cc_final: 0.4351 (mmt) REVERT: R 130 PHE cc_start: 0.8332 (m-10) cc_final: 0.7627 (m-80) REVERT: R 305 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7584 (t160) REVERT: S 3 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: S 160 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7988 (ttp80) REVERT: S 202 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7888 (ptp90) REVERT: S 223 ASP cc_start: 0.7278 (m-30) cc_final: 0.6742 (m-30) REVERT: T 15 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8817 (pttm) REVERT: T 129 ARG cc_start: 0.8321 (ttt90) cc_final: 0.8108 (ttt90) REVERT: T 155 ASN cc_start: 0.8400 (t0) cc_final: 0.7916 (t0) REVERT: T 264 TYR cc_start: 0.9108 (m-80) cc_final: 0.8521 (m-80) outliers start: 21 outliers final: 12 residues processed: 199 average time/residue: 0.2188 time to fit residues: 59.1577 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 : 1.024 ------------------------------------------------------------------------------- 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 228 LEU 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 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 259 GLN Chi-restraints excluded: chain T residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136199 restraints weight = 10590.214| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.40 r_work: 0.3255 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3582 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= 0.141 Angle : 0.601 8.986 12457 Z= 0.307 Chirality : 0.043 0.152 1422 Planarity : 0.004 0.044 1569 Dihedral : 4.476 54.752 1248 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.65 % Allowed : 20.72 % Favored : 77.63 % 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: -0.33 (0.25), residues: 1130 helix: 0.94 (0.28), residues: 350 sheet: -0.50 (0.31), residues: 293 loop : -0.80 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 107 HIS 0.003 0.001 HIS T 91 PHE 0.020 0.001 PHE I 335 TYR 0.012 0.001 TYR I 303 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 371) hydrogen bonds : angle 4.34334 ( 1059) SS BOND : bond 0.00659 ( 5) SS BOND : angle 1.42166 ( 10) covalent geometry : bond 0.00327 ( 9176) covalent geometry : angle 0.59992 (12447) *********************** 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 205 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8285 (pmm) cc_final: 0.7851 (pmm) REVERT: I 24 ARG cc_start: 0.7453 (mtp-110) cc_final: 0.6968 (mtm110) REVERT: I 26 ASP cc_start: 0.7304 (m-30) cc_final: 0.7070 (m-30) REVERT: I 217 GLU cc_start: 0.7599 (pt0) cc_final: 0.7199 (pt0) REVERT: I 346 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7248 (ttmt) REVERT: R 41 MET cc_start: 0.5101 (mtt) cc_final: 0.4317 (mmm) REVERT: R 130 PHE cc_start: 0.8353 (m-10) cc_final: 0.7650 (m-80) REVERT: S 160 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7996 (ttp80) REVERT: S 202 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7873 (ptp90) REVERT: S 223 ASP cc_start: 0.7295 (m-30) cc_final: 0.6757 (m-30) REVERT: T 155 ASN cc_start: 0.8449 (t0) cc_final: 0.7959 (t0) REVERT: T 264 TYR cc_start: 0.9111 (m-80) cc_final: 0.8699 (m-80) outliers start: 16 outliers final: 9 residues processed: 196 average time/residue: 0.2317 time to fit residues: 62.3240 Evaluate side-chains 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.202536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134756 restraints weight = 10631.054| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.42 r_work: 0.3262 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9181 Z= 0.157 Angle : 0.627 9.564 12457 Z= 0.318 Chirality : 0.044 0.196 1422 Planarity : 0.004 0.044 1569 Dihedral : 4.608 55.004 1248 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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 : 0.00 % 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: -0.39 (0.25), residues: 1130 helix: 1.04 (0.28), residues: 343 sheet: -0.45 (0.31), residues: 277 loop : -1.00 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.003 0.001 HIS S 35 PHE 0.025 0.001 PHE R 105 TYR 0.020 0.001 TYR I 303 ARG 0.008 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 371) hydrogen bonds : angle 4.40100 ( 1059) SS BOND : bond 0.00419 ( 5) SS BOND : angle 2.44032 ( 10) covalent geometry : bond 0.00368 ( 9176) covalent geometry : angle 0.62323 (12447) ********************** 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 195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.8264 (pmm) cc_final: 0.7820 (pmm) REVERT: I 24 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.7054 (mtm110) REVERT: I 26 ASP cc_start: 0.7250 (m-30) cc_final: 0.7014 (m-30) REVERT: I 217 GLU cc_start: 0.7647 (pt0) cc_final: 0.7247 (pt0) REVERT: I 346 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7229 (ttmt) REVERT: R 41 MET cc_start: 0.5067 (mtt) cc_final: 0.4303 (mmm) REVERT: R 130 PHE cc_start: 0.8355 (m-10) cc_final: 0.7670 (m-80) REVERT: S 160 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8048 (ttp80) REVERT: S 202 ARG cc_start: 0.8224 (ptp90) cc_final: 0.8001 (ptp-170) REVERT: S 223 ASP cc_start: 0.7338 (m-30) cc_final: 0.6519 (m-30) REVERT: T 220 GLN cc_start: 0.7996 (mt0) cc_final: 0.7649 (mt0) REVERT: T 264 TYR cc_start: 0.9106 (m-80) cc_final: 0.8887 (m-80) outliers start: 14 outliers final: 12 residues processed: 188 average time/residue: 0.2238 time to fit residues: 57.3653 Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain G residue 25 ILE 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 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: 0.8980 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 14 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 256 ASN ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4305 r_free = 0.4305 target = 0.204605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131518 restraints weight = 10596.011| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.91 r_work: 0.3339 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9181 Z= 0.121 Angle : 0.601 8.171 12457 Z= 0.304 Chirality : 0.042 0.156 1422 Planarity : 0.004 0.042 1569 Dihedral : 4.513 55.197 1248 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.93 % Allowed : 21.44 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1130 helix: 1.11 (0.28), residues: 338 sheet: -0.38 (0.32), residues: 277 loop : -0.96 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 82 HIS 0.002 0.000 HIS R 152 PHE 0.023 0.001 PHE R 105 TYR 0.017 0.001 TYR I 303 ARG 0.003 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 371) hydrogen bonds : angle 4.30028 ( 1059) SS BOND : bond 0.00433 ( 5) SS BOND : angle 1.98107 ( 10) covalent geometry : bond 0.00277 ( 9176) covalent geometry : angle 0.59841 (12447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.02 seconds wall clock time: 98 minutes 9.68 seconds (5889.68 seconds total)