Starting phenix.real_space_refine on Thu Mar 13 08:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk6_33888/03_2025/7yk6_33888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk6_33888/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yk6_33888/03_2025/7yk6_33888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk6_33888/03_2025/7yk6_33888.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk6_33888/03_2025/7yk6_33888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk6_33888/03_2025/7yk6_33888.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.34, per 1000 atoms: 0.61 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.95 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: 2.24 Time building geometry restraints manager: 2.59 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: 1.170 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.090 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- 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 8927 Z= 0.397 Angle : 0.734 18.678 12109 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 (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: -0.18 (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 TRP 0.021 0.002 TRP T 169 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.002 PHE T 253 TYR 0.027 0.002 TYR S 235 ARG 0.008 0.001 ARG T 129 *********************** 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 : 0.835 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: 0.2386 time to fit residues: 61.8730 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 : 0.969 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.152252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129646 restraints weight = 13656.058| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.56 r_work: 0.3553 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8927 Z= 0.240 Angle : 0.661 20.717 12109 Z= 0.327 Chirality : 0.044 0.149 1374 Planarity : 0.005 0.073 1528 Dihedral : 6.829 85.618 1217 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 1.07 % Allowed : 10.98 % Favored : 87.95 % 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: 0.15 (0.26), residues: 1098 helix: 1.96 (0.28), residues: 362 sheet: -0.12 (0.32), residues: 296 loop : -1.34 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 268 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.002 PHE I 251 TYR 0.013 0.001 TYR S 235 ARG 0.005 0.000 ARG T 251 *********************** 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 225 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: I 9 ASP cc_start: 0.7691 (m-30) cc_final: 0.7466 (m-30) REVERT: I 17 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7610 (mtpt) REVERT: I 25 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7443 (mm-30) REVERT: I 29 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7875 (ttmm) REVERT: I 38 LEU cc_start: 0.8389 (tt) cc_final: 0.8134 (tt) REVERT: I 39 LEU cc_start: 0.8211 (mt) cc_final: 0.8002 (mm) REVERT: I 210 LYS cc_start: 0.8231 (tmmt) cc_final: 0.7966 (tmmt) REVERT: R 39 ARG cc_start: 0.7549 (ptp90) cc_final: 0.7260 (mtm-85) REVERT: R 192 LEU cc_start: 0.8212 (tp) cc_final: 0.7971 (tp) REVERT: R 208 ARG cc_start: 0.8382 (tmm-80) cc_final: 0.7995 (tmm-80) REVERT: T 34 THR cc_start: 0.7858 (t) cc_final: 0.7477 (t) REVERT: T 61 MET cc_start: 0.8081 (ppp) cc_final: 0.7488 (ppp) REVERT: T 86 THR cc_start: 0.8729 (p) cc_final: 0.8527 (p) REVERT: T 150 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.8249 (mpt180) REVERT: T 189 SER cc_start: 0.8396 (p) cc_final: 0.8083 (t) REVERT: T 230 ASN cc_start: 0.8092 (m110) cc_final: 0.7753 (m-40) REVERT: T 258 ASP cc_start: 0.7795 (t0) cc_final: 0.7356 (t0) outliers start: 10 outliers final: 8 residues processed: 218 average time/residue: 0.2395 time to fit residues: 69.1354 Evaluate side-chains 214 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 97 VAL 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 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.149547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126331 restraints weight = 13870.298| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.62 r_work: 0.3495 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8927 Z= 0.424 Angle : 0.688 17.684 12109 Z= 0.349 Chirality : 0.047 0.155 1374 Planarity : 0.005 0.061 1528 Dihedral : 6.866 88.366 1216 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 1.92 % Allowed : 14.07 % Favored : 84.01 % 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: 0.01 (0.26), residues: 1098 helix: 1.67 (0.28), residues: 368 sheet: -0.05 (0.32), residues: 289 loop : -1.40 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.019 0.002 PHE S 29 TYR 0.020 0.002 TYR S 190 ARG 0.005 0.001 ARG T 314 *********************** 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 235 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 17 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7671 (mtpt) REVERT: I 29 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7819 (ttmm) REVERT: I 38 LEU cc_start: 0.8432 (tt) cc_final: 0.8142 (tt) REVERT: I 53 MET cc_start: 0.0101 (pmm) cc_final: -0.1887 (pmm) REVERT: I 198 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7457 (mttm) REVERT: I 210 LYS cc_start: 0.8270 (tmmt) cc_final: 0.8009 (tmmt) REVERT: R 39 ARG cc_start: 0.7605 (ptp90) cc_final: 0.7073 (mtm-85) REVERT: R 125 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.6849 (m) REVERT: R 208 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8037 (tmm-80) REVERT: T 49 ARG cc_start: 0.8397 (mmt180) cc_final: 0.8162 (mpt180) REVERT: T 61 MET cc_start: 0.8149 (ppp) cc_final: 0.7658 (ppp) REVERT: T 189 SER cc_start: 0.8339 (p) cc_final: 0.8080 (t) REVERT: T 230 ASN cc_start: 0.8234 (m110) cc_final: 0.7818 (m110) REVERT: T 239 ASN cc_start: 0.8178 (m-40) cc_final: 0.7931 (m-40) REVERT: T 258 ASP cc_start: 0.7864 (t0) cc_final: 0.7238 (t0) outliers start: 18 outliers final: 13 residues processed: 222 average time/residue: 0.2451 time to fit residues: 71.5437 Evaluate side-chains 221 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN 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 = 0.152353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129168 restraints weight = 13700.600| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.62 r_work: 0.3558 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8927 Z= 0.196 Angle : 0.573 11.260 12109 Z= 0.292 Chirality : 0.043 0.166 1374 Planarity : 0.004 0.052 1528 Dihedral : 6.519 89.674 1216 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.77 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1098 helix: 1.83 (0.28), residues: 364 sheet: 0.01 (0.32), residues: 295 loop : -1.29 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE R 283 TYR 0.015 0.001 TYR S 235 ARG 0.005 0.000 ARG T 219 *********************** 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 242 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 210 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7978 (tmmt) REVERT: R 39 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7101 (mtm-85) REVERT: R 107 TRP cc_start: 0.5870 (t-100) cc_final: 0.5253 (t-100) REVERT: R 192 LEU cc_start: 0.8284 (tp) cc_final: 0.8061 (tp) REVERT: R 208 ARG cc_start: 0.8398 (tmm-80) cc_final: 0.7994 (tmm-80) REVERT: S 45 LEU cc_start: 0.8326 (mt) cc_final: 0.8097 (mp) REVERT: T 49 ARG cc_start: 0.8338 (mmt180) cc_final: 0.8135 (mpt180) REVERT: T 61 MET cc_start: 0.8144 (ppp) cc_final: 0.7725 (ppp) REVERT: T 86 THR cc_start: 0.8829 (p) cc_final: 0.8582 (p) REVERT: T 189 SER cc_start: 0.8380 (p) cc_final: 0.8097 (t) REVERT: T 230 ASN cc_start: 0.8145 (m110) cc_final: 0.7759 (m-40) REVERT: T 239 ASN cc_start: 0.8145 (m-40) cc_final: 0.7876 (m-40) REVERT: T 258 ASP cc_start: 0.7916 (t0) cc_final: 0.7231 (t0) outliers start: 26 outliers final: 15 residues processed: 228 average time/residue: 0.2462 time to fit residues: 74.1829 Evaluate side-chains 223 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 141 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127911 restraints weight = 13722.364| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.64 r_work: 0.3538 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8927 Z= 0.282 Angle : 0.599 10.715 12109 Z= 0.306 Chirality : 0.044 0.170 1374 Planarity : 0.004 0.053 1528 Dihedral : 6.507 87.344 1216 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.99 % Allowed : 17.48 % Favored : 79.53 % 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: 0.09 (0.26), residues: 1098 helix: 1.67 (0.27), residues: 373 sheet: -0.01 (0.32), residues: 297 loop : -1.33 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE T 199 TYR 0.016 0.002 TYR S 190 ARG 0.008 0.000 ARG T 251 *********************** 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 241 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 35 LYS cc_start: 0.8310 (mttt) cc_final: 0.8106 (mttm) REVERT: I 210 LYS cc_start: 0.8230 (tmmt) cc_final: 0.8012 (tmmt) REVERT: R 39 ARG cc_start: 0.7525 (ptp90) cc_final: 0.7324 (mtm-85) REVERT: R 107 TRP cc_start: 0.5913 (t-100) cc_final: 0.5310 (t-100) REVERT: R 192 LEU cc_start: 0.8306 (tp) cc_final: 0.8068 (tp) REVERT: R 208 ARG cc_start: 0.8392 (tmm-80) cc_final: 0.7991 (tmm-80) REVERT: T 49 ARG cc_start: 0.8358 (mmt180) cc_final: 0.8149 (mpt180) REVERT: T 61 MET cc_start: 0.8167 (ppp) cc_final: 0.7762 (ppp) REVERT: T 86 THR cc_start: 0.8888 (p) cc_final: 0.8656 (p) REVERT: T 189 SER cc_start: 0.8427 (p) cc_final: 0.8158 (t) REVERT: T 230 ASN cc_start: 0.8199 (m110) cc_final: 0.7833 (m110) REVERT: T 239 ASN cc_start: 0.8154 (m-40) cc_final: 0.7902 (m-40) outliers start: 28 outliers final: 18 residues processed: 227 average time/residue: 0.2457 time to fit residues: 73.7486 Evaluate side-chains 229 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 114 CYS Chi-restraints excluded: chain R residue 254 SER Chi-restraints excluded: chain S residue 11 LEU 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 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 234 PHE 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 87 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129462 restraints weight = 13649.920| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.58 r_work: 0.3559 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8927 Z= 0.224 Angle : 0.599 16.321 12109 Z= 0.300 Chirality : 0.044 0.173 1374 Planarity : 0.004 0.054 1528 Dihedral : 6.422 86.008 1216 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.99 % Allowed : 18.34 % Favored : 78.68 % 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: 0.13 (0.26), residues: 1098 helix: 1.70 (0.27), residues: 370 sheet: 0.09 (0.32), residues: 289 loop : -1.33 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE T 253 TYR 0.015 0.001 TYR S 235 ARG 0.007 0.000 ARG T 251 *********************** 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 236 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 35 LYS cc_start: 0.8308 (mttt) cc_final: 0.8099 (mttm) REVERT: I 38 LEU cc_start: 0.8450 (tt) cc_final: 0.8151 (tt) REVERT: I 210 LYS cc_start: 0.8275 (tmmt) cc_final: 0.8050 (tmmt) REVERT: I 346 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7751 (ttpt) REVERT: R 39 ARG cc_start: 0.7547 (ptp90) cc_final: 0.7035 (mtm-85) REVERT: R 107 TRP cc_start: 0.5919 (t-100) cc_final: 0.5309 (t-100) REVERT: R 125 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.6918 (m) REVERT: R 192 LEU cc_start: 0.8310 (tp) cc_final: 0.8059 (tp) REVERT: R 208 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.8155 (tmm-80) REVERT: T 61 MET cc_start: 0.8099 (ppp) cc_final: 0.7703 (ppp) REVERT: T 86 THR cc_start: 0.8835 (p) cc_final: 0.8596 (p) REVERT: T 150 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.8291 (mpt180) REVERT: T 189 SER cc_start: 0.8430 (p) cc_final: 0.8158 (t) REVERT: T 230 ASN cc_start: 0.8169 (m110) cc_final: 0.7783 (m-40) REVERT: T 239 ASN cc_start: 0.8149 (m-40) cc_final: 0.7947 (m-40) REVERT: T 290 ASP cc_start: 0.7688 (m-30) cc_final: 0.7289 (m-30) outliers start: 28 outliers final: 17 residues processed: 221 average time/residue: 0.3030 time to fit residues: 89.9239 Evaluate side-chains 222 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 R residue 78 THR 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 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 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 79 optimal weight: 0.0970 chunk 73 optimal weight: 0.0670 chunk 98 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130269 restraints weight = 13713.845| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.67 r_work: 0.3578 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8927 Z= 0.164 Angle : 0.563 14.339 12109 Z= 0.283 Chirality : 0.042 0.182 1374 Planarity : 0.004 0.053 1528 Dihedral : 6.161 83.262 1216 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.99 % Allowed : 18.34 % Favored : 78.68 % 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: 0.27 (0.26), residues: 1098 helix: 1.83 (0.27), residues: 368 sheet: 0.14 (0.32), residues: 288 loop : -1.22 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 283 TYR 0.010 0.001 TYR R 140 ARG 0.006 0.000 ARG T 251 *********************** 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 233 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7673 (tmm) cc_final: 0.7364 (tmm) REVERT: I 35 LYS cc_start: 0.8280 (mttt) cc_final: 0.8051 (mttm) REVERT: I 38 LEU cc_start: 0.8500 (tt) cc_final: 0.8232 (tt) REVERT: I 210 LYS cc_start: 0.8269 (tmmt) cc_final: 0.8024 (tmmt) REVERT: I 346 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7747 (ttpt) REVERT: R 39 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7117 (mtm-85) REVERT: R 125 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7351 (t) REVERT: R 192 LEU cc_start: 0.8310 (tp) cc_final: 0.8063 (tp) REVERT: T 22 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7570 (mtt-85) REVERT: T 61 MET cc_start: 0.8095 (ppp) cc_final: 0.7714 (ppp) REVERT: T 150 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8305 (mpt180) REVERT: T 189 SER cc_start: 0.8438 (p) cc_final: 0.8148 (t) REVERT: T 230 ASN cc_start: 0.8140 (m110) cc_final: 0.7755 (m-40) REVERT: T 239 ASN cc_start: 0.8120 (m-40) cc_final: 0.7860 (m-40) REVERT: T 290 ASP cc_start: 0.7687 (m-30) cc_final: 0.7398 (m-30) outliers start: 28 outliers final: 21 residues processed: 218 average time/residue: 0.2454 time to fit residues: 70.5806 Evaluate side-chains 226 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 78 THR 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 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 183 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 ASN S 194 ASN T 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129949 restraints weight = 13852.501| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.71 r_work: 0.3571 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8927 Z= 0.174 Angle : 0.562 14.262 12109 Z= 0.282 Chirality : 0.042 0.185 1374 Planarity : 0.004 0.053 1528 Dihedral : 5.974 78.796 1216 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 19.62 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1098 helix: 1.92 (0.27), residues: 367 sheet: 0.15 (0.32), residues: 287 loop : -1.18 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE T 278 TYR 0.010 0.001 TYR S 235 ARG 0.005 0.000 ARG T 251 *********************** 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 224 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7655 (tmm) cc_final: 0.7359 (tmm) REVERT: G 38 MET cc_start: 0.8358 (ttp) cc_final: 0.8147 (ttm) REVERT: I 35 LYS cc_start: 0.8241 (mttt) cc_final: 0.8018 (mttm) REVERT: I 38 LEU cc_start: 0.8512 (tt) cc_final: 0.8245 (tt) REVERT: I 210 LYS cc_start: 0.8266 (tmmt) cc_final: 0.8020 (tmmt) REVERT: I 311 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7767 (tp) REVERT: I 313 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7467 (mmtm) REVERT: I 346 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7753 (ttpt) REVERT: R 39 ARG cc_start: 0.7530 (ptp90) cc_final: 0.7132 (mtm-85) REVERT: R 125 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.6915 (m) REVERT: R 192 LEU cc_start: 0.8279 (tp) cc_final: 0.8036 (tp) REVERT: R 294 THR cc_start: 0.8267 (p) cc_final: 0.8054 (t) REVERT: T 22 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7279 (mtt-85) REVERT: T 61 MET cc_start: 0.8133 (ppp) cc_final: 0.7760 (ppp) REVERT: T 86 THR cc_start: 0.8710 (p) cc_final: 0.8447 (p) REVERT: T 150 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8317 (mpt180) REVERT: T 189 SER cc_start: 0.8372 (p) cc_final: 0.8093 (t) REVERT: T 230 ASN cc_start: 0.8131 (m110) cc_final: 0.7739 (m-40) REVERT: T 239 ASN cc_start: 0.8111 (m-40) cc_final: 0.7859 (m-40) REVERT: T 258 ASP cc_start: 0.7890 (t0) cc_final: 0.7311 (t0) REVERT: T 290 ASP cc_start: 0.7587 (m-30) cc_final: 0.7290 (m-30) outliers start: 23 outliers final: 18 residues processed: 213 average time/residue: 0.2488 time to fit residues: 69.5285 Evaluate side-chains 223 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 78 THR 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 183 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.151880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128371 restraints weight = 13782.629| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.66 r_work: 0.3528 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8927 Z= 0.267 Angle : 0.618 18.363 12109 Z= 0.309 Chirality : 0.044 0.197 1374 Planarity : 0.004 0.054 1528 Dihedral : 6.057 75.071 1216 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.77 % Allowed : 19.72 % Favored : 77.51 % 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: 0.21 (0.26), residues: 1098 helix: 1.76 (0.27), residues: 374 sheet: 0.10 (0.32), residues: 289 loop : -1.28 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE S 212 TYR 0.017 0.001 TYR S 190 ARG 0.010 0.000 ARG T 251 *********************** 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 233 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7629 (tmm) cc_final: 0.7307 (tmm) REVERT: G 38 MET cc_start: 0.8359 (ttp) cc_final: 0.8144 (ttm) REVERT: I 35 LYS cc_start: 0.8301 (mttt) cc_final: 0.8075 (mttm) REVERT: I 38 LEU cc_start: 0.8515 (tt) cc_final: 0.8229 (tt) REVERT: I 210 LYS cc_start: 0.8282 (tmmt) cc_final: 0.8036 (tmmt) REVERT: I 346 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7735 (ttpt) REVERT: R 39 ARG cc_start: 0.7528 (ptp90) cc_final: 0.7207 (mtm-85) REVERT: R 125 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.6886 (m) REVERT: R 192 LEU cc_start: 0.8324 (tp) cc_final: 0.8055 (tp) REVERT: R 193 LEU cc_start: 0.8186 (tt) cc_final: 0.7949 (mt) REVERT: T 61 MET cc_start: 0.8127 (ppp) cc_final: 0.7582 (ppp) REVERT: T 150 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8251 (mpt180) REVERT: T 189 SER cc_start: 0.8457 (p) cc_final: 0.8137 (t) REVERT: T 230 ASN cc_start: 0.8146 (m110) cc_final: 0.7707 (m-40) REVERT: T 239 ASN cc_start: 0.8120 (m-40) cc_final: 0.7872 (m-40) REVERT: T 258 ASP cc_start: 0.7925 (t0) cc_final: 0.6990 (t0) REVERT: T 290 ASP cc_start: 0.7601 (m-30) cc_final: 0.7266 (m-30) outliers start: 26 outliers final: 22 residues processed: 220 average time/residue: 0.2674 time to fit residues: 76.5500 Evaluate side-chains 230 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 215 CYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 114 CYS 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 183 GLN 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 269 ILE 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 26 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.152427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128967 restraints weight = 13736.425| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.65 r_work: 0.3537 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8927 Z= 0.238 Angle : 0.612 17.627 12109 Z= 0.307 Chirality : 0.044 0.309 1374 Planarity : 0.004 0.054 1528 Dihedral : 6.041 73.064 1216 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.45 % Allowed : 20.26 % Favored : 77.29 % 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: 0.25 (0.26), residues: 1098 helix: 1.86 (0.27), residues: 368 sheet: 0.09 (0.32), residues: 289 loop : -1.26 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE I 260 TYR 0.013 0.001 TYR S 190 ARG 0.010 0.000 ARG T 251 ********************** 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 229 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7631 (tmm) cc_final: 0.7307 (tmm) REVERT: G 38 MET cc_start: 0.8370 (ttp) cc_final: 0.8152 (ttm) REVERT: I 35 LYS cc_start: 0.8305 (mttt) cc_final: 0.8082 (mttm) REVERT: I 38 LEU cc_start: 0.8529 (tt) cc_final: 0.8251 (tt) REVERT: I 192 PHE cc_start: 0.8805 (t80) cc_final: 0.8261 (t80) REVERT: I 193 LYS cc_start: 0.8693 (mttt) cc_final: 0.8413 (mttt) REVERT: I 210 LYS cc_start: 0.8338 (tmmt) cc_final: 0.8097 (tmmt) REVERT: I 346 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7759 (ttpt) REVERT: R 39 ARG cc_start: 0.7499 (ptp90) cc_final: 0.7076 (mtm-85) REVERT: R 125 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7369 (t) REVERT: R 192 LEU cc_start: 0.8323 (tp) cc_final: 0.8054 (tp) REVERT: R 193 LEU cc_start: 0.8169 (tt) cc_final: 0.7800 (mp) REVERT: T 61 MET cc_start: 0.8114 (ppp) cc_final: 0.7567 (ppp) REVERT: T 150 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8258 (mpt180) REVERT: T 189 SER cc_start: 0.8467 (p) cc_final: 0.8146 (t) REVERT: T 230 ASN cc_start: 0.8111 (m110) cc_final: 0.7717 (m-40) REVERT: T 239 ASN cc_start: 0.8133 (m-40) cc_final: 0.7881 (m-40) REVERT: T 258 ASP cc_start: 0.7910 (t0) cc_final: 0.7002 (t0) REVERT: T 290 ASP cc_start: 0.7597 (m-30) cc_final: 0.7280 (m-30) outliers start: 23 outliers final: 22 residues processed: 218 average time/residue: 0.2404 time to fit residues: 69.4370 Evaluate side-chains 227 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 215 CYS Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 114 CYS 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 183 GLN 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 269 ILE 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 21 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129364 restraints weight = 13759.253| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.60 r_work: 0.3547 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8927 Z= 0.244 Angle : 0.618 17.538 12109 Z= 0.310 Chirality : 0.045 0.290 1374 Planarity : 0.004 0.054 1528 Dihedral : 6.002 71.131 1216 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.56 % Allowed : 19.94 % Favored : 77.51 % 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: 0.24 (0.26), residues: 1098 helix: 1.79 (0.27), residues: 372 sheet: 0.09 (0.32), residues: 289 loop : -1.23 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 268 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE I 260 TYR 0.014 0.001 TYR S 190 ARG 0.010 0.000 ARG T 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4814.21 seconds wall clock time: 85 minutes 10.51 seconds (5110.51 seconds total)