Starting phenix.real_space_refine on Sat Aug 23 00:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk6_33888/08_2025/7yk6_33888.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 1 4.86 5 C 5575 2.51 5 N 1497 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8736 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1694 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 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} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'IYF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8736 At special positions: 0 Unit cell: (91.035, 118.881, 131.733, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 55 16.00 O 1608 8.00 N 1497 7.00 C 5575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 337.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.148A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'I' and resid 6 through 30 Processing helix chain 'I' and resid 45 through 53 removed outlier: 4.331A pdb=" N MET I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 214 removed outlier: 4.172A pdb=" N HIS I 214 " --> pdb=" O LYS I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 243 through 256 Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.601A pdb=" N PHE I 275 " --> pdb=" O LYS I 271 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 299 through 312 removed outlier: 3.683A pdb=" N ASN I 312 " --> pdb=" O PHE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 352 removed outlier: 3.789A pdb=" N PHE I 335 " --> pdb=" O LYS I 331 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL I 336 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 Processing helix chain 'R' and resid 75 through 103 removed outlier: 4.381A pdb=" N PHE R 79 " --> pdb=" O PRO R 75 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 110 through 144 removed outlier: 4.266A pdb=" N LYS R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 180 Proline residue: R 175 - end of helix Processing helix chain 'R' and resid 202 through 212 Processing helix chain 'R' and resid 213 through 233 removed outlier: 3.662A pdb=" N ARG R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 275 removed outlier: 3.876A pdb=" N ARG R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) Proline residue: R 261 - end of helix Processing helix chain 'R' and resid 282 through 300 Proline residue: R 292 - end of helix removed outlier: 3.626A pdb=" N SER R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 320 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.601A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.116A 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 62 through 65 removed outlier: 3.756A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.525A pdb=" N CYS T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 35 Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 191 removed outlier: 3.751A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS I 225 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE I 265 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.573A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU S 20 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.506A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.552A pdb=" N ILE S 216 " --> pdb=" O VAL S 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.981A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 46 through 52 removed outlier: 3.630A pdb=" N ARG T 46 " --> pdb=" O ASN T 340 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN T 340 " --> pdb=" O ARG T 46 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.649A 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: 6.957A pdb=" N ALA T 73 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET T 61 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL T 71 " --> pdb=" O MET T 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP T 63 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU T 69 " --> pdb=" O TRP T 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 100 through 105 removed outlier: 3.795A pdb=" N GLY T 115 " --> pdb=" O THR T 102 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) removed outlier: 3.615A 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: 6.760A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR T 178 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 187 through 192 removed outlier: 6.921A pdb=" N GLY T 202 " --> pdb=" O MET T 188 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU T 190 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL T 200 " --> pdb=" O LEU T 190 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU T 192 " --> pdb=" O LEU T 198 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU T 198 " --> pdb=" O LEU T 192 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER T 207 " --> pdb=" O ALA T 203 " (cutoff:3.500A) removed outlier: 3.761A 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: 4.079A pdb=" N THR T 249 " --> pdb=" O SER T 245 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS T 250 " --> pdb=" O THR T 263 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR T 263 " --> pdb=" O CYS T 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU T 252 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN T 259 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 276 through 278 400 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2811 1.34 - 1.46: 2135 1.46 - 1.58: 3902 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8927 Sorted by residual: bond pdb=" C10 IYF R 601 " pdb=" N11 IYF R 601 " ideal model delta sigma weight residual 1.274 1.475 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C27 IYF R 601 " pdb=" N26 IYF R 601 " ideal model delta sigma weight residual 1.374 1.503 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C25 IYF R 601 " pdb=" C9 IYF R 601 " ideal model delta sigma weight residual 1.376 1.271 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C10 IYF R 601 " pdb=" C9 IYF R 601 " ideal model delta sigma weight residual 1.444 1.549 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C13 IYF R 601 " pdb=" N12 IYF R 601 " ideal model delta sigma weight residual 1.380 1.483 -0.103 2.00e-02 2.50e+03 2.64e+01 ... (remaining 8922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 12058 3.74 - 7.47: 39 7.47 - 11.21: 9 11.21 - 14.94: 1 14.94 - 18.68: 2 Bond angle restraints: 12109 Sorted by residual: angle pdb=" N PHE R 324 " pdb=" CA PHE R 324 " pdb=" C PHE R 324 " ideal model delta sigma weight residual 112.23 104.25 7.98 1.26e+00 6.30e-01 4.01e+01 angle pdb=" C25 IYF R 601 " pdb=" C9 IYF R 601 " pdb=" C8 IYF R 601 " ideal model delta sigma weight residual 106.34 125.02 -18.68 3.00e+00 1.11e-01 3.88e+01 angle pdb=" C13 IYF R 601 " pdb=" N15 IYF R 601 " pdb=" C16 IYF R 601 " ideal model delta sigma weight residual 126.12 110.40 15.72 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C9 IYF R 601 " pdb=" C10 IYF R 601 " pdb=" N11 IYF R 601 " ideal model delta sigma weight residual 121.60 110.73 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C LEU R 193 " pdb=" N ARG R 194 " pdb=" CA ARG R 194 " ideal model delta sigma weight residual 121.54 114.92 6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4714 17.20 - 34.41: 422 34.41 - 51.61: 89 51.61 - 68.82: 12 68.82 - 86.02: 13 Dihedral angle restraints: 5250 sinusoidal: 2021 harmonic: 3229 Sorted by residual: dihedral pdb=" CA TRP R 200 " pdb=" C TRP R 200 " pdb=" N LEU R 201 " pdb=" CA LEU R 201 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LEU R 193 " pdb=" C LEU R 193 " pdb=" N ARG R 194 " pdb=" CA ARG R 194 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG R 198 " pdb=" C ARG R 198 " pdb=" N TYR R 199 " pdb=" CA TYR R 199 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 5247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1210 0.072 - 0.144: 160 0.144 - 0.216: 3 0.216 - 0.288: 0 0.288 - 0.360: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA THR R 323 " pdb=" N THR R 323 " pdb=" C THR R 323 " pdb=" CB THR R 323 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA PHE R 324 " pdb=" N PHE R 324 " pdb=" C PHE R 324 " pdb=" CB PHE R 324 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ARG I 32 " pdb=" N ARG I 32 " pdb=" C ARG I 32 " pdb=" CB ARG I 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1371 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 IYF R 601 " -0.127 2.00e-02 2.50e+03 3.79e-01 2.15e+03 pdb=" C16 IYF R 601 " 0.554 2.00e-02 2.50e+03 pdb=" N11 IYF R 601 " 0.318 2.00e-02 2.50e+03 pdb=" N12 IYF R 601 " -0.318 2.00e-02 2.50e+03 pdb=" N14 IYF R 601 " 0.136 2.00e-02 2.50e+03 pdb=" N15 IYF R 601 " -0.563 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IYF R 601 " 0.259 2.00e-02 2.50e+03 2.69e-01 7.23e+02 pdb=" C9 IYF R 601 " -0.255 2.00e-02 2.50e+03 pdb=" N11 IYF R 601 " 0.278 2.00e-02 2.50e+03 pdb=" N12 IYF R 601 " -0.282 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.077 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO S 148 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.061 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 191 2.68 - 3.24: 8542 3.24 - 3.79: 13454 3.79 - 4.35: 17695 4.35 - 4.90: 29830 Nonbonded interactions: 69712 Sorted by model distance: nonbonded pdb=" O THR R 282 " pdb=" OG1 THR R 285 " model vdw 2.130 3.040 nonbonded pdb=" OG SER T 245 " pdb=" OD1 ASP T 247 " model vdw 2.158 3.040 nonbonded pdb=" OG SER T 161 " pdb=" OD1 ASP T 163 " model vdw 2.166 3.040 nonbonded pdb=" OG SER T 331 " pdb=" OD1 ASP T 333 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASP T 153 " pdb=" N ASP T 154 " model vdw 2.207 3.120 ... (remaining 69707 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.201 8929 Z= 0.283 Angle : 0.735 18.678 12113 Z= 0.380 Chirality : 0.046 0.360 1374 Planarity : 0.013 0.379 1528 Dihedral : 14.225 86.020 3160 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 0.21 % Allowed : 0.85 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1098 helix: 1.79 (0.28), residues: 358 sheet: -0.56 (0.32), residues: 297 loop : -1.38 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 129 TYR 0.027 0.002 TYR S 235 PHE 0.013 0.002 PHE T 253 TRP 0.021 0.002 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 8927) covalent geometry : angle 0.73417 (12109) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.76234 ( 4) hydrogen bonds : bond 0.17996 ( 400) hydrogen bonds : angle 6.90847 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: I 17 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7344 (mtpt) REVERT: I 29 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7825 (ttmm) REVERT: I 38 LEU cc_start: 0.8082 (tt) cc_final: 0.7827 (tt) REVERT: R 107 TRP cc_start: 0.5507 (t-100) cc_final: 0.5071 (t-100) REVERT: T 61 MET cc_start: 0.7881 (ppp) cc_final: 0.7266 (ppp) REVERT: T 150 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.8049 (mpt180) REVERT: T 230 ASN cc_start: 0.7899 (m110) cc_final: 0.7678 (m-40) outliers start: 2 outliers final: 1 residues processed: 197 average time/residue: 0.1052 time to fit residues: 27.0993 Evaluate side-chains 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 GLN T 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129540 restraints weight = 13771.761| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.57 r_work: 0.3549 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8929 Z= 0.163 Angle : 0.661 19.602 12113 Z= 0.327 Chirality : 0.044 0.150 1374 Planarity : 0.005 0.072 1528 Dihedral : 6.815 85.018 1217 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 0.96 % Allowed : 10.98 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1098 helix: 1.98 (0.28), residues: 361 sheet: -0.12 (0.32), residues: 296 loop : -1.35 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 251 TYR 0.014 0.001 TYR S 190 PHE 0.017 0.002 PHE I 251 TRP 0.017 0.001 TRP R 268 HIS 0.003 0.001 HIS T 225 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8927) covalent geometry : angle 0.66089 (12109) SS BOND : bond 0.00590 ( 2) SS BOND : angle 1.20826 ( 4) hydrogen bonds : bond 0.04752 ( 400) hydrogen bonds : angle 5.02861 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: I 9 ASP cc_start: 0.7697 (m-30) cc_final: 0.7474 (m-30) REVERT: I 17 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7618 (mtpt) REVERT: I 25 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7449 (mm-30) REVERT: I 29 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7873 (ttmm) REVERT: I 38 LEU cc_start: 0.8388 (tt) cc_final: 0.8133 (tt) REVERT: I 39 LEU cc_start: 0.8211 (mt) cc_final: 0.8002 (mm) REVERT: I 210 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7971 (tmmt) REVERT: R 39 ARG cc_start: 0.7559 (ptp90) cc_final: 0.7266 (mtm-85) REVERT: R 192 LEU cc_start: 0.8218 (tp) cc_final: 0.7977 (tp) REVERT: R 208 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.7995 (tmm-80) REVERT: S 217 SER cc_start: 0.8498 (m) cc_final: 0.8127 (p) REVERT: T 34 THR cc_start: 0.7857 (t) cc_final: 0.7478 (t) REVERT: T 61 MET cc_start: 0.8085 (ppp) cc_final: 0.7495 (ppp) REVERT: T 86 THR cc_start: 0.8730 (p) cc_final: 0.8520 (p) REVERT: T 150 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8252 (mpt180) REVERT: T 189 SER cc_start: 0.8392 (p) cc_final: 0.8082 (t) REVERT: T 230 ASN cc_start: 0.8090 (m110) cc_final: 0.7742 (m-40) REVERT: T 258 ASP cc_start: 0.7800 (t0) cc_final: 0.7357 (t0) outliers start: 9 outliers final: 7 residues processed: 220 average time/residue: 0.0979 time to fit residues: 28.8627 Evaluate side-chains 217 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 210 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128728 restraints weight = 13650.102| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.63 r_work: 0.3552 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8929 Z= 0.158 Angle : 0.597 14.783 12113 Z= 0.303 Chirality : 0.043 0.150 1374 Planarity : 0.005 0.059 1528 Dihedral : 6.568 89.317 1216 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 1.92 % Allowed : 13.54 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1098 helix: 1.94 (0.28), residues: 362 sheet: -0.04 (0.32), residues: 294 loop : -1.34 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 49 TYR 0.013 0.001 TYR S 235 PHE 0.014 0.001 PHE S 29 TRP 0.015 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8927) covalent geometry : angle 0.59661 (12109) SS BOND : bond 0.00705 ( 2) SS BOND : angle 1.36861 ( 4) hydrogen bonds : bond 0.04334 ( 400) hydrogen bonds : angle 4.67239 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 25 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7484 (mm-30) REVERT: I 29 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7955 (ttmm) REVERT: I 38 LEU cc_start: 0.8414 (tt) cc_final: 0.8138 (tt) REVERT: I 53 MET cc_start: -0.0015 (pmm) cc_final: -0.1920 (pmm) REVERT: I 210 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7998 (tmmt) REVERT: R 39 ARG cc_start: 0.7568 (ptp90) cc_final: 0.7092 (mtm-85) REVERT: R 107 TRP cc_start: 0.5831 (t-100) cc_final: 0.5310 (t-100) REVERT: R 208 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.8015 (tmm-80) REVERT: S 217 SER cc_start: 0.8439 (m) cc_final: 0.8090 (p) REVERT: T 34 THR cc_start: 0.7841 (t) cc_final: 0.7477 (t) REVERT: T 61 MET cc_start: 0.8094 (ppp) cc_final: 0.7629 (ppp) REVERT: T 86 THR cc_start: 0.8727 (p) cc_final: 0.8495 (p) REVERT: T 189 SER cc_start: 0.8388 (p) cc_final: 0.8095 (t) REVERT: T 230 ASN cc_start: 0.8181 (m110) cc_final: 0.7874 (m-40) REVERT: T 239 ASN cc_start: 0.8124 (m-40) cc_final: 0.7861 (m-40) REVERT: T 258 ASP cc_start: 0.7841 (t0) cc_final: 0.7287 (t0) outliers start: 18 outliers final: 14 residues processed: 218 average time/residue: 0.1004 time to fit residues: 28.9940 Evaluate side-chains 224 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.0570 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129319 restraints weight = 13873.051| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8929 Z= 0.160 Angle : 0.579 11.586 12113 Z= 0.296 Chirality : 0.043 0.153 1374 Planarity : 0.004 0.058 1528 Dihedral : 6.500 89.904 1216 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 2.77 % Allowed : 15.35 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.26), residues: 1098 helix: 1.94 (0.28), residues: 362 sheet: -0.04 (0.32), residues: 300 loop : -1.32 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 48 TYR 0.013 0.001 TYR S 190 PHE 0.014 0.001 PHE S 29 TRP 0.015 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8927) covalent geometry : angle 0.57861 (12109) SS BOND : bond 0.00692 ( 2) SS BOND : angle 1.33209 ( 4) hydrogen bonds : bond 0.04177 ( 400) hydrogen bonds : angle 4.58200 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 198 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7558 (ttmm) REVERT: I 210 LYS cc_start: 0.8248 (tmmt) cc_final: 0.8034 (tmmt) REVERT: R 39 ARG cc_start: 0.7543 (ptp90) cc_final: 0.7091 (mtm-85) REVERT: R 107 TRP cc_start: 0.5878 (t-100) cc_final: 0.5348 (t-100) REVERT: R 125 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.6917 (m) REVERT: R 192 LEU cc_start: 0.8240 (tp) cc_final: 0.8024 (tp) REVERT: R 208 ARG cc_start: 0.8371 (tmm-80) cc_final: 0.7989 (tmm-80) REVERT: S 217 SER cc_start: 0.8450 (m) cc_final: 0.8106 (p) REVERT: T 34 THR cc_start: 0.7873 (t) cc_final: 0.7522 (t) REVERT: T 50 THR cc_start: 0.8448 (m) cc_final: 0.8131 (t) REVERT: T 61 MET cc_start: 0.8092 (ppp) cc_final: 0.7672 (ppp) REVERT: T 86 THR cc_start: 0.8749 (p) cc_final: 0.8497 (p) REVERT: T 189 SER cc_start: 0.8379 (p) cc_final: 0.8092 (t) REVERT: T 230 ASN cc_start: 0.8172 (m110) cc_final: 0.7828 (m-40) REVERT: T 239 ASN cc_start: 0.8143 (m-40) cc_final: 0.7888 (m-40) REVERT: T 258 ASP cc_start: 0.7890 (t0) cc_final: 0.7302 (t0) outliers start: 26 outliers final: 16 residues processed: 226 average time/residue: 0.1139 time to fit residues: 34.0439 Evaluate side-chains 226 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 0.0000 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.129686 restraints weight = 13838.246| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.68 r_work: 0.3565 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8929 Z= 0.123 Angle : 0.551 8.133 12113 Z= 0.284 Chirality : 0.042 0.152 1374 Planarity : 0.004 0.055 1528 Dihedral : 6.365 88.992 1216 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.09 % Allowed : 16.20 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1098 helix: 2.03 (0.28), residues: 361 sheet: 0.03 (0.32), residues: 294 loop : -1.29 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 48 TYR 0.012 0.001 TYR S 190 PHE 0.012 0.001 PHE R 283 TRP 0.015 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8927) covalent geometry : angle 0.55049 (12109) SS BOND : bond 0.00603 ( 2) SS BOND : angle 1.18366 ( 4) hydrogen bonds : bond 0.03827 ( 400) hydrogen bonds : angle 4.44762 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 25 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7473 (mm-30) REVERT: I 210 LYS cc_start: 0.8274 (tmmt) cc_final: 0.8038 (tmmt) REVERT: I 220 THR cc_start: 0.8365 (m) cc_final: 0.8163 (m) REVERT: I 346 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7731 (ttpt) REVERT: R 39 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7127 (mtm-85) REVERT: R 107 TRP cc_start: 0.5888 (t-100) cc_final: 0.5234 (t-100) REVERT: R 125 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7371 (t) REVERT: R 192 LEU cc_start: 0.8257 (tp) cc_final: 0.8015 (tp) REVERT: R 208 ARG cc_start: 0.8403 (tmm-80) cc_final: 0.7999 (tmm-80) REVERT: S 217 SER cc_start: 0.8434 (m) cc_final: 0.8092 (p) REVERT: T 50 THR cc_start: 0.8417 (m) cc_final: 0.8112 (t) REVERT: T 61 MET cc_start: 0.8113 (ppp) cc_final: 0.7699 (ppp) REVERT: T 86 THR cc_start: 0.8727 (p) cc_final: 0.8451 (p) REVERT: T 150 ARG cc_start: 0.8573 (mmt-90) cc_final: 0.8313 (mpt180) REVERT: T 189 SER cc_start: 0.8392 (p) cc_final: 0.8090 (t) REVERT: T 230 ASN cc_start: 0.8167 (m110) cc_final: 0.7768 (m-40) REVERT: T 239 ASN cc_start: 0.8126 (m-40) cc_final: 0.7853 (m-40) REVERT: T 258 ASP cc_start: 0.7915 (t0) cc_final: 0.7276 (t0) outliers start: 29 outliers final: 17 residues processed: 217 average time/residue: 0.1060 time to fit residues: 30.1562 Evaluate side-chains 223 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.153986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130497 restraints weight = 13807.344| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.68 r_work: 0.3577 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8929 Z= 0.113 Angle : 0.551 16.333 12113 Z= 0.278 Chirality : 0.042 0.162 1374 Planarity : 0.004 0.052 1528 Dihedral : 6.178 86.224 1216 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.45 % Allowed : 17.38 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1098 helix: 1.94 (0.27), residues: 365 sheet: 0.03 (0.32), residues: 294 loop : -1.22 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 219 TYR 0.013 0.001 TYR S 235 PHE 0.011 0.001 PHE R 283 TRP 0.013 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8927) covalent geometry : angle 0.55022 (12109) SS BOND : bond 0.00533 ( 2) SS BOND : angle 1.18758 ( 4) hydrogen bonds : bond 0.03668 ( 400) hydrogen bonds : angle 4.36557 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7655 (tmm) cc_final: 0.7356 (tmm) REVERT: G 38 MET cc_start: 0.8392 (ttp) cc_final: 0.8180 (ttm) REVERT: I 9 ASP cc_start: 0.7718 (m-30) cc_final: 0.7458 (m-30) REVERT: I 25 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7506 (mm-30) REVERT: I 210 LYS cc_start: 0.8267 (tmmt) cc_final: 0.8029 (tmmt) REVERT: I 346 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7743 (ttpt) REVERT: R 39 ARG cc_start: 0.7557 (ptp90) cc_final: 0.7096 (mtm-85) REVERT: R 107 TRP cc_start: 0.5897 (t-100) cc_final: 0.5270 (t-100) REVERT: R 192 LEU cc_start: 0.8271 (tp) cc_final: 0.8042 (tp) REVERT: R 208 ARG cc_start: 0.8325 (tmm-80) cc_final: 0.8096 (tmm-80) REVERT: S 217 SER cc_start: 0.8434 (m) cc_final: 0.8087 (p) REVERT: T 61 MET cc_start: 0.8122 (ppp) cc_final: 0.7711 (ppp) REVERT: T 86 THR cc_start: 0.8685 (p) cc_final: 0.8413 (p) REVERT: T 150 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8330 (mpt180) REVERT: T 189 SER cc_start: 0.8387 (p) cc_final: 0.8090 (t) REVERT: T 230 ASN cc_start: 0.8177 (m110) cc_final: 0.7793 (m-40) REVERT: T 239 ASN cc_start: 0.8118 (m-40) cc_final: 0.7856 (m-40) REVERT: T 258 ASP cc_start: 0.7881 (t0) cc_final: 0.7115 (t0) outliers start: 23 outliers final: 19 residues processed: 217 average time/residue: 0.1083 time to fit residues: 30.8984 Evaluate side-chains 226 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129281 restraints weight = 13839.204| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.68 r_work: 0.3548 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8929 Z= 0.147 Angle : 0.568 14.931 12113 Z= 0.287 Chirality : 0.043 0.181 1374 Planarity : 0.004 0.053 1528 Dihedral : 6.115 82.251 1216 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.67 % Allowed : 18.12 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1098 helix: 1.89 (0.27), residues: 368 sheet: 0.09 (0.32), residues: 288 loop : -1.23 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 219 TYR 0.013 0.001 TYR S 190 PHE 0.013 0.001 PHE S 68 TRP 0.014 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8927) covalent geometry : angle 0.56717 (12109) SS BOND : bond 0.00683 ( 2) SS BOND : angle 1.32918 ( 4) hydrogen bonds : bond 0.03863 ( 400) hydrogen bonds : angle 4.37976 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7608 (tmm) cc_final: 0.7277 (tmm) REVERT: G 38 MET cc_start: 0.8420 (ttp) cc_final: 0.8211 (ttm) REVERT: I 210 LYS cc_start: 0.8288 (tmmt) cc_final: 0.8041 (tmmt) REVERT: I 346 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7742 (ttpt) REVERT: R 39 ARG cc_start: 0.7502 (ptp90) cc_final: 0.7175 (mtm-85) REVERT: R 125 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7391 (t) REVERT: R 192 LEU cc_start: 0.8289 (tp) cc_final: 0.8039 (tp) REVERT: R 193 LEU cc_start: 0.8181 (tt) cc_final: 0.7956 (mt) REVERT: R 208 ARG cc_start: 0.8358 (tmm-80) cc_final: 0.8123 (tmm-80) REVERT: S 217 SER cc_start: 0.8371 (m) cc_final: 0.8021 (p) REVERT: T 61 MET cc_start: 0.8133 (ppp) cc_final: 0.7768 (ppp) REVERT: T 86 THR cc_start: 0.8769 (p) cc_final: 0.8503 (p) REVERT: T 150 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.8326 (mpt180) REVERT: T 189 SER cc_start: 0.8444 (p) cc_final: 0.8153 (t) REVERT: T 230 ASN cc_start: 0.8182 (m110) cc_final: 0.7804 (m-40) REVERT: T 239 ASN cc_start: 0.8116 (m-40) cc_final: 0.7857 (m-40) REVERT: T 258 ASP cc_start: 0.7896 (t0) cc_final: 0.7095 (t0) REVERT: T 290 ASP cc_start: 0.7702 (m-30) cc_final: 0.7383 (m-30) outliers start: 25 outliers final: 19 residues processed: 217 average time/residue: 0.1183 time to fit residues: 33.5438 Evaluate side-chains 220 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129454 restraints weight = 13701.123| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.63 r_work: 0.3561 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8929 Z= 0.150 Angle : 0.573 14.200 12113 Z= 0.290 Chirality : 0.043 0.197 1374 Planarity : 0.004 0.052 1528 Dihedral : 6.071 78.652 1216 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.56 % Allowed : 18.34 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1098 helix: 1.82 (0.27), residues: 372 sheet: 0.09 (0.32), residues: 289 loop : -1.21 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 219 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE I 224 TRP 0.013 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8927) covalent geometry : angle 0.57270 (12109) SS BOND : bond 0.00705 ( 2) SS BOND : angle 1.30827 ( 4) hydrogen bonds : bond 0.03879 ( 400) hydrogen bonds : angle 4.40514 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7574 (tmm) cc_final: 0.7264 (tmm) REVERT: G 38 MET cc_start: 0.8469 (ttp) cc_final: 0.8265 (ttm) REVERT: I 210 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8089 (tmmt) REVERT: I 313 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7469 (mmtm) REVERT: I 346 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7757 (ttpt) REVERT: R 39 ARG cc_start: 0.7556 (ptp90) cc_final: 0.7165 (mtm-85) REVERT: R 125 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7392 (t) REVERT: R 192 LEU cc_start: 0.8293 (tp) cc_final: 0.8033 (tp) REVERT: R 193 LEU cc_start: 0.8185 (tt) cc_final: 0.7957 (mt) REVERT: R 208 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.8119 (tmm-80) REVERT: S 217 SER cc_start: 0.8438 (m) cc_final: 0.8099 (p) REVERT: T 61 MET cc_start: 0.8112 (ppp) cc_final: 0.7552 (ppp) REVERT: T 86 THR cc_start: 0.8784 (p) cc_final: 0.8518 (p) REVERT: T 150 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8291 (mpt180) REVERT: T 189 SER cc_start: 0.8468 (p) cc_final: 0.8145 (t) REVERT: T 230 ASN cc_start: 0.8167 (m110) cc_final: 0.7803 (m-40) REVERT: T 239 ASN cc_start: 0.8131 (m-40) cc_final: 0.7873 (m-40) REVERT: T 258 ASP cc_start: 0.7889 (t0) cc_final: 0.7082 (t0) REVERT: T 290 ASP cc_start: 0.7696 (m-30) cc_final: 0.7470 (m-30) outliers start: 24 outliers final: 20 residues processed: 209 average time/residue: 0.1224 time to fit residues: 33.2302 Evaluate side-chains 220 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130133 restraints weight = 13733.760| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.59 r_work: 0.3568 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8929 Z= 0.146 Angle : 0.587 18.014 12113 Z= 0.294 Chirality : 0.043 0.192 1374 Planarity : 0.004 0.051 1528 Dihedral : 6.022 75.708 1216 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.77 % Allowed : 18.44 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1098 helix: 1.84 (0.27), residues: 372 sheet: 0.09 (0.32), residues: 289 loop : -1.20 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 219 TYR 0.013 0.001 TYR S 190 PHE 0.012 0.001 PHE T 253 TRP 0.012 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8927) covalent geometry : angle 0.58626 (12109) SS BOND : bond 0.00738 ( 2) SS BOND : angle 1.36261 ( 4) hydrogen bonds : bond 0.03847 ( 400) hydrogen bonds : angle 4.38568 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7566 (tmm) cc_final: 0.7267 (tmm) REVERT: G 38 MET cc_start: 0.8473 (ttp) cc_final: 0.8270 (ttm) REVERT: I 210 LYS cc_start: 0.8336 (tmmt) cc_final: 0.8095 (tmmt) REVERT: I 313 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7464 (mmtm) REVERT: I 346 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7757 (ttpt) REVERT: R 39 ARG cc_start: 0.7480 (ptp90) cc_final: 0.7172 (mtm-85) REVERT: R 125 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7381 (t) REVERT: R 192 LEU cc_start: 0.8263 (tp) cc_final: 0.8018 (tp) REVERT: R 193 LEU cc_start: 0.8184 (tt) cc_final: 0.7944 (mt) REVERT: T 61 MET cc_start: 0.8109 (ppp) cc_final: 0.7550 (ppp) REVERT: T 86 THR cc_start: 0.8790 (p) cc_final: 0.8526 (p) REVERT: T 150 ARG cc_start: 0.8579 (mmt-90) cc_final: 0.8295 (mpt180) REVERT: T 189 SER cc_start: 0.8488 (p) cc_final: 0.8147 (t) REVERT: T 230 ASN cc_start: 0.8167 (m110) cc_final: 0.7799 (m-40) REVERT: T 239 ASN cc_start: 0.8127 (m-40) cc_final: 0.7872 (m-40) REVERT: T 258 ASP cc_start: 0.7889 (t0) cc_final: 0.7081 (t0) REVERT: T 290 ASP cc_start: 0.7690 (m-30) cc_final: 0.7459 (m-30) outliers start: 26 outliers final: 23 residues processed: 210 average time/residue: 0.1214 time to fit residues: 33.3543 Evaluate side-chains 223 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.153058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129578 restraints weight = 13578.405| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.64 r_work: 0.3562 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8929 Z= 0.147 Angle : 0.593 17.443 12113 Z= 0.296 Chirality : 0.044 0.331 1374 Planarity : 0.004 0.050 1528 Dihedral : 5.978 73.025 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.67 % Allowed : 18.87 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1098 helix: 1.83 (0.27), residues: 372 sheet: 0.10 (0.32), residues: 289 loop : -1.22 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 219 TYR 0.013 0.001 TYR S 190 PHE 0.013 0.001 PHE T 253 TRP 0.019 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8927) covalent geometry : angle 0.59229 (12109) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.40226 ( 4) hydrogen bonds : bond 0.03844 ( 400) hydrogen bonds : angle 4.39178 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7574 (tmm) cc_final: 0.7310 (tmm) REVERT: G 38 MET cc_start: 0.8471 (ttp) cc_final: 0.8269 (ttm) REVERT: I 210 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8089 (tmmt) REVERT: I 313 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7466 (mmtm) REVERT: I 346 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7769 (ttpt) REVERT: R 39 ARG cc_start: 0.7527 (ptp90) cc_final: 0.7125 (mtm-85) REVERT: R 125 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.6930 (m) REVERT: R 192 LEU cc_start: 0.8288 (tp) cc_final: 0.8051 (tp) REVERT: T 61 MET cc_start: 0.8116 (ppp) cc_final: 0.7554 (ppp) REVERT: T 86 THR cc_start: 0.8785 (p) cc_final: 0.8538 (p) REVERT: T 150 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8282 (mpt180) REVERT: T 189 SER cc_start: 0.8481 (p) cc_final: 0.8145 (t) REVERT: T 230 ASN cc_start: 0.8168 (m110) cc_final: 0.7809 (m-40) REVERT: T 239 ASN cc_start: 0.8130 (m-40) cc_final: 0.7878 (m-40) REVERT: T 258 ASP cc_start: 0.7891 (t0) cc_final: 0.7076 (t0) REVERT: T 290 ASP cc_start: 0.7600 (m-30) cc_final: 0.7275 (m-30) outliers start: 25 outliers final: 23 residues processed: 209 average time/residue: 0.1189 time to fit residues: 32.5964 Evaluate side-chains 223 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 179 GLN T 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128983 restraints weight = 13649.207| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.67 r_work: 0.3537 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8929 Z= 0.170 Angle : 0.611 17.561 12113 Z= 0.307 Chirality : 0.044 0.316 1374 Planarity : 0.004 0.051 1528 Dihedral : 6.022 71.168 1216 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.77 % Allowed : 18.87 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.26), residues: 1098 helix: 1.83 (0.27), residues: 372 sheet: 0.09 (0.32), residues: 289 loop : -1.26 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 251 TYR 0.015 0.001 TYR S 190 PHE 0.013 0.001 PHE T 234 TRP 0.018 0.001 TRP T 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8927) covalent geometry : angle 0.61069 (12109) SS BOND : bond 0.00852 ( 2) SS BOND : angle 1.69839 ( 4) hydrogen bonds : bond 0.03991 ( 400) hydrogen bonds : angle 4.43990 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.28 seconds wall clock time: 39 minutes 19.16 seconds (2359.16 seconds total)