Starting phenix.real_space_refine on Fri Oct 23 01:53:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.map" model { file = "/net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9spg_55084/10_2026/9spg_55084.cif" } resolution = 3.47 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 4746 2.51 5 N 1384 2.21 5 O 1398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7536 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2435 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 336} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 6, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2414 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 4, 'TRANS': 336} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 9} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2400 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 4, 'TRANS': 336} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 7, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 287 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 1.73, per 1000 atoms: 0.23 Number of scatterers: 7536 At special positions: 0 Unit cell: (95, 97.85, 91.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1398 8.00 N 1384 7.00 C 4746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 63 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 395.1 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 7.7% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.696A pdb=" N TYR A 312 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.699A pdb=" N LYS B 48 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.690A pdb=" N GLU B 135 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.937A pdb=" N ALA B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.520A pdb=" N GLY C 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'D' and resid 54 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.580A pdb=" N GLY A 104 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 190 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 215 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.615A pdb=" N GLY A 355 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 251 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS A 262 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 235 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 215 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 234 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 213 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 215 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 52 through 56 current: chain 'B' and resid 74 through 83 removed outlier: 6.949A pdb=" N PHE B 202 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR B 245 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 204 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 243 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR B 206 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 241 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 208 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS B 239 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE B 210 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN B 237 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS B 212 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP B 235 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 262 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 279 " --> pdb=" O HIS B 298 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN B 316 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 302 through 304 removed outlier: 4.085A pdb=" N ALA B 302 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 56 removed outlier: 3.615A pdb=" N VAL C 333 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR C 258 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS C 262 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP C 235 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP C 215 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS C 234 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR C 213 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 240 " --> pdb=" O ALA C 207 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1134 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: 1.22 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1241 1.27 - 1.41: 2113 1.41 - 1.54: 4309 1.54 - 1.68: 7 1.68 - 1.81: 14 Bond restraints: 7684 Sorted by residual: bond pdb=" C LYS B 349 " pdb=" O LYS B 349 " ideal model delta sigma weight residual 1.234 1.140 0.095 1.15e-02 7.56e+03 6.77e+01 bond pdb=" C GLU B 348 " pdb=" O GLU B 348 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.24e-02 6.50e+03 3.88e+01 bond pdb=" C GLU A 81 " pdb=" N GLN A 82 " ideal model delta sigma weight residual 1.329 1.394 -0.065 1.37e-02 5.33e+03 2.26e+01 bond pdb=" C TYR A 323 " pdb=" O TYR A 323 " ideal model delta sigma weight residual 1.236 1.180 0.055 1.20e-02 6.94e+03 2.13e+01 bond pdb=" CA LYS B 217 " pdb=" C LYS B 217 " ideal model delta sigma weight residual 1.531 1.506 0.025 5.40e-03 3.43e+04 2.08e+01 ... (remaining 7679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 10128 2.38 - 4.76: 225 4.76 - 7.14: 53 7.14 - 9.52: 4 9.52 - 11.90: 4 Bond angle restraints: 10414 Sorted by residual: angle pdb=" N LYS B 217 " pdb=" CA LYS B 217 " pdb=" C LYS B 217 " ideal model delta sigma weight residual 108.75 99.15 9.60 9.60e-01 1.09e+00 1.00e+02 angle pdb=" CA PHE A 325 " pdb=" CB PHE A 325 " pdb=" CG PHE A 325 " ideal model delta sigma weight residual 113.80 122.52 -8.72 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA TYR A 323 " pdb=" C TYR A 323 " pdb=" O TYR A 323 " ideal model delta sigma weight residual 120.36 113.59 6.77 1.08e+00 8.57e-01 3.93e+01 angle pdb=" C PHE A 325 " pdb=" N SER A 326 " pdb=" CA SER A 326 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N ASN B 219 " pdb=" CA ASN B 219 " pdb=" C ASN B 219 " ideal model delta sigma weight residual 112.59 105.22 7.37 1.22e+00 6.72e-01 3.65e+01 ... (remaining 10409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4124 17.30 - 34.59: 208 34.59 - 51.88: 37 51.88 - 69.18: 11 69.18 - 86.47: 3 Dihedral angle restraints: 4383 sinusoidal: 1390 harmonic: 2993 Sorted by residual: dihedral pdb=" CA GLY C 306 " pdb=" C GLY C 306 " pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LYS A 37 " pdb=" CB LYS A 37 " pdb=" CG LYS A 37 " pdb=" CD LYS A 37 " ideal model delta sinusoidal sigma weight residual -180.00 -120.69 -59.31 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASN B 95 " pdb=" C ASN B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 164.72 15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 917 0.057 - 0.113: 153 0.113 - 0.170: 47 0.170 - 0.227: 8 0.227 - 0.284: 3 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA GLU D 24 " pdb=" N GLU D 24 " pdb=" C GLU D 24 " pdb=" CB GLU D 24 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ASN B 269 " pdb=" N ASN B 269 " pdb=" C ASN B 269 " pdb=" CB ASN B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1125 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 216 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C LEU B 216 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU B 216 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS B 217 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 215 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASP B 215 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP B 215 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU B 216 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 347 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR B 347 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 347 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 348 " 0.019 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 32 2.59 - 3.16: 5855 3.16 - 3.74: 9493 3.74 - 4.32: 13209 4.32 - 4.90: 24954 Nonbonded interactions: 53543 Sorted by model distance: nonbonded pdb=" O ASP C 322 " pdb=" OD1 ASP C 322 " model vdw 2.007 3.040 nonbonded pdb=" O THR C 329 " pdb=" OG SER C 330 " model vdw 2.277 3.040 nonbonded pdb=" N LYS C 272 " pdb=" O LYS C 272 " model vdw 2.365 2.496 nonbonded pdb=" OD1 ASP B 324 " pdb=" OG SER B 330 " model vdw 2.391 3.040 nonbonded pdb=" N GLN B 82 " pdb=" OE1 GLN B 82 " model vdw 2.406 3.120 ... (remaining 53538 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 36 or (resid 37 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 and (na \ me N or name CA or name C or name O or name CB )) or (resid 46 through 49 and (n \ ame N or name CA or name C or name O or name CB )) or resid 50 through 64 or (re \ sid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 or ( \ resid 67 and (name N or name CA or name C or name O or name CB )) or resid 68 th \ rough 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) o \ r resid 71 through 108 or (resid 109 and (name N or name CA or name C or name O \ or name CB )) or resid 110 through 119 or (resid 120 and (name N or name CA or n \ ame C or name O or name CB )) or resid 121 through 125 or (resid 126 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 through 1 \ 32 or (resid 133 and (name N or name CA or name C or name O or name CB )) or res \ id 134 through 147 or (resid 148 and (name N or name CA or name C or name O or n \ ame CB )) or resid 149 through 155 or (resid 156 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 or (resid 159 through 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 172 o \ r (resid 173 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 74 through 183 or (resid 184 through 186 and (name N or name CA or name C or nam \ e O or name CB )) or resid 187 through 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 195 or (resid 196 and (na \ me N or name CA or name C or name O or name CB )) or resid 197 through 221 or (r \ esid 222 through 225 and (name N or name CA or name C or name O or name CB )) or \ resid 226 through 247 or (resid 248 through 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 262 or (resid 263 through 265 and \ (name N or name CA or name C or name O or name CB )) or (resid 266 through 269 \ and (name N or name CA or name C or name O or name CB )) or resid 270 through 27 \ 1 or (resid 272 through 273 and (name N or name CA or name C or name O or name C \ B )) or resid 274 or (resid 275 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 285 or (resid 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 349 or (resid 350 through 351 and \ (name N or name CA or name C or name O or name CB )) or resid 352 through 360)) selection = (chain 'B' and (resid 20 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 68 or (resid 69 through 70 and (na \ me N or name CA or name C or name O or name CB )) or resid 71 through 74 or (res \ id 75 through 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 90 or (resid 91 and (name N or name CA or name C or name O or name \ CB )) or resid 92 through 129 or (resid 130 and (name N or name CA or name C or \ name O or name CB )) or resid 131 through 147 or (resid 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 t \ hrough 159 or (resid 160 through 161 and (name N or name CA or name C or name O \ or name CB )) or resid 162 through 175 or (resid 176 through 179 and (name N or \ name CA or name C or name O or name CB )) or resid 180 through 183 or (resid 184 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 87 through 195 or (resid 196 and (name N or name CA or name C or name O or name \ CB )) or resid 197 through 214 or (resid 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 220 or (resid 221 through 225 and (na \ me N or name CA or name C or name O or name CB )) or resid 226 through 231 or (r \ esid 232 and (name N or name CA or name C or name O or name CB )) or resid 233 t \ hrough 262 or (resid 263 through 265 and (name N or name CA or name C or name O \ or name CB )) or resid 266 through 271 or (resid 272 through 273 and (name N or \ name CA or name C or name O or name CB )) or resid 274 through 285 or (resid 286 \ and (name N or name CA or name C or name O or name CB )) or resid 287 through 3 \ 25 or (resid 326 through 327 and (name N or name CA or name C or name O or name \ CB )) or resid 328 through 360)) selection = (chain 'C' and (resid 20 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or (resid 46 through 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 52 or (resid 53 and (name N or na \ me CA or name C or name O or name CB )) or resid 54 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 68 or ( \ resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 74 or (resid 75 through 76 and (name N or name CA or name C or \ name O or name CB )) or resid 77 through 88 or (resid 89 through 91 and (name N \ or name CA or name C or name O or name CB )) or resid 92 through 125 or (resid 1 \ 26 through 127 and (name N or name CA or name C or name O or name CB )) or resid \ 128 through 132 or (resid 133 and (name N or name CA or name C or name O or nam \ e CB )) or resid 134 through 158 or (resid 159 through 161 and (name N or name C \ A or name C or name O or name CB )) or resid 162 through 172 or (resid 173 and ( \ name N or name CA or name C or name O or name CB )) or resid 174 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB )) or resid 191 \ through 214 or (resid 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 231 or (resid 232 and (name N or name CA or name C or n \ ame O or name CB )) or resid 233 through 268 or (resid 269 and (name N or name C \ A or name C or name O or name CB )) or resid 270 through 304 or (resid 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 325 or \ (resid 326 through 327 and (name N or name CA or name C or name O or name CB )) \ or resid 328 through 349 or (resid 350 through 351 and (name N or name CA or nam \ e C or name O or name CB )) or resid 352 through 360)) } 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.200 Find NCS groups from input model: 0.160 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.095 7685 Z= 0.383 Angle : 0.896 11.904 10416 Z= 0.602 Chirality : 0.053 0.284 1128 Planarity : 0.007 0.124 1373 Dihedral : 11.627 86.474 2510 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.24 % Rotamer: Outliers : 0.16 % Allowed : 9.34 % Favored : 90.50 % 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 are not related in a simple way. whole: -1.31 (0.25), residues: 1062 helix: -1.29 (0.83), residues: 27 sheet: -0.22 (0.22), residues: 588 loop : -1.68 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.013 0.002 TYR A 323 PHE 0.053 0.001 PHE A 325 TRP 0.011 0.002 TRP A 337 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.38 ( 7684) covalent geometry : angle 0.89622 / 0.60 (10414) SS BOND : bond 0.00150 / 0.08 ( 1) SS BOND : angle 0.64524 / 0.34 ( 2) hydrogen bonds : bond 0.13619 / 9.17 ( 416) hydrogen bonds : angle 6.02118 / 4.10 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.8851 (tmm) cc_final: 0.8520 (tmm) REVERT: B 235 ASP cc_start: 0.8588 (t0) cc_final: 0.8329 (t0) REVERT: B 263 ASN cc_start: 0.8198 (t0) cc_final: 0.7834 (t0) REVERT: C 124 ASN cc_start: 0.9166 (m-40) cc_final: 0.8935 (m-40) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0509 time to fit residues: 3.3590 Evaluate side-chains 39 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 270 GLN B 270 GLN B 289 ASN C 298 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146333 restraints weight = 7525.227| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.39 r_work: 0.3560 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7685 Z= 0.172 Angle : 0.586 6.227 10416 Z= 0.333 Chirality : 0.046 0.172 1128 Planarity : 0.003 0.047 1373 Dihedral : 4.498 36.390 1168 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.45 % Allowed : 9.50 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.26), residues: 1062 helix: -0.88 (0.92), residues: 27 sheet: 0.33 (0.23), residues: 555 loop : -1.70 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.012 0.002 TYR A 236 PHE 0.020 0.001 PHE A 325 TRP 0.011 0.001 TRP C 337 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7684) covalent geometry : angle 0.58594 / 0.33 (10414) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.65837 / 0.35 ( 2) hydrogen bonds : bond 0.05086 / 3.50 ( 416) hydrogen bonds : angle 4.96466 / 3.35 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.262 Fit side-chains REVERT: A 37 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8261 (tmtt) REVERT: A 190 SER cc_start: 0.8620 (p) cc_final: 0.8353 (m) REVERT: B 196 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8004 (tttm) REVERT: B 235 ASP cc_start: 0.8354 (t0) cc_final: 0.8002 (t0) REVERT: B 263 ASN cc_start: 0.8085 (t0) cc_final: 0.7768 (t0) REVERT: C 124 ASN cc_start: 0.9158 (m-40) cc_final: 0.8933 (m-40) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.0655 time to fit residues: 5.5549 Evaluate side-chains 46 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [71, 44, 94, 13, 89, 101, 64, 90, 74, 93, 60] chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144189 restraints weight = 7491.126| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.51 r_work: 0.3538 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7685 Z= 0.176 Angle : 0.571 5.029 10416 Z= 0.327 Chirality : 0.045 0.159 1128 Planarity : 0.003 0.048 1373 Dihedral : 4.392 27.309 1168 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.58 % Allowed : 10.63 % Favored : 86.80 % 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 are not related in a simple way. whole: -0.83 (0.26), residues: 1062 helix: -0.93 (0.95), residues: 27 sheet: 0.33 (0.23), residues: 564 loop : -1.65 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.012 0.001 TYR C 312 PHE 0.019 0.001 PHE A 325 TRP 0.011 0.001 TRP B 337 HIS 0.003 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 7684) covalent geometry : angle 0.57072 / 0.33 (10414) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.72460 / 0.38 ( 2) hydrogen bonds : bond 0.05123 / 3.51 ( 416) hydrogen bonds : angle 4.86965 / 3.29 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.247 Fit side-chains REVERT: A 37 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (tmtt) REVERT: A 190 SER cc_start: 0.8677 (p) cc_final: 0.8463 (m) REVERT: B 124 ASN cc_start: 0.9099 (m110) cc_final: 0.8890 (m110) REVERT: B 196 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8006 (tttp) REVERT: B 235 ASP cc_start: 0.8319 (t0) cc_final: 0.8026 (t0) REVERT: B 263 ASN cc_start: 0.8135 (t0) cc_final: 0.7781 (t0) REVERT: C 124 ASN cc_start: 0.9207 (m-40) cc_final: 0.8978 (m-40) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.0506 time to fit residues: 4.4923 Evaluate side-chains 48 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [15, 99, 2, 103, 33, 72, 70, 41, 97, 68, 30] chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137883 restraints weight = 8232.299| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.27 r_work: 0.3534 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7685 Z= 0.123 Angle : 0.513 4.646 10416 Z= 0.294 Chirality : 0.044 0.149 1128 Planarity : 0.003 0.046 1373 Dihedral : 4.114 21.781 1168 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 11.92 % Favored : 85.99 % 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 are not related in a simple way. whole: -0.64 (0.26), residues: 1062 helix: -0.89 (0.94), residues: 27 sheet: 0.54 (0.23), residues: 558 loop : -1.62 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 145 TYR 0.009 0.001 TYR A 236 PHE 0.013 0.001 PHE A 325 TRP 0.009 0.001 TRP C 337 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7684) covalent geometry : angle 0.51328 / 0.29 (10414) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.45365 / 0.24 ( 2) hydrogen bonds : bond 0.04315 / 2.97 ( 416) hydrogen bonds : angle 4.74968 / 3.21 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7982 (tmtt) REVERT: A 235 ASP cc_start: 0.8349 (t0) cc_final: 0.8060 (t0) REVERT: B 235 ASP cc_start: 0.8205 (t0) cc_final: 0.7827 (t0) REVERT: B 263 ASN cc_start: 0.8114 (t0) cc_final: 0.7714 (t0) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.0620 time to fit residues: 5.1782 Evaluate side-chains 50 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [42, 46, 70, 98, 94, 37, 40, 51, 105, 12, 0] chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134160 restraints weight = 8305.351| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.25 r_work: 0.3479 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7685 Z= 0.215 Angle : 0.592 5.267 10416 Z= 0.341 Chirality : 0.045 0.152 1128 Planarity : 0.003 0.049 1373 Dihedral : 4.356 18.861 1167 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.90 % Allowed : 12.24 % Favored : 84.86 % 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 are not related in a simple way. whole: -0.77 (0.26), residues: 1062 helix: -1.05 (0.96), residues: 27 sheet: 0.47 (0.23), residues: 558 loop : -1.72 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.015 0.002 TYR C 312 PHE 0.022 0.002 PHE A 325 TRP 0.013 0.002 TRP A 337 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 7684) covalent geometry : angle 0.59236 / 0.34 (10414) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.94569 / 0.50 ( 2) hydrogen bonds : bond 0.05487 / 3.75 ( 416) hydrogen bonds : angle 4.89845 / 3.31 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8076 (tmtt) REVERT: A 190 SER cc_start: 0.8927 (p) cc_final: 0.8669 (m) REVERT: A 235 ASP cc_start: 0.8422 (t0) cc_final: 0.8152 (t0) REVERT: B 235 ASP cc_start: 0.8362 (t0) cc_final: 0.8110 (t0) REVERT: B 263 ASN cc_start: 0.8301 (t0) cc_final: 0.7918 (t0) REVERT: C 124 ASN cc_start: 0.9305 (m-40) cc_final: 0.9018 (m-40) outliers start: 18 outliers final: 16 residues processed: 57 average time/residue: 0.0557 time to fit residues: 5.0904 Evaluate side-chains 55 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [55, 46, 1, 89, 47, 103, 14, 100, 48, 25, 72] chunk 55 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 1 optimal weight: 0.3980 chunk 89 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138477 restraints weight = 8158.780| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.25 r_work: 0.3548 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7685 Z= 0.107 Angle : 0.491 4.796 10416 Z= 0.282 Chirality : 0.043 0.144 1128 Planarity : 0.002 0.048 1373 Dihedral : 3.959 18.847 1167 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.58 % Allowed : 12.72 % Favored : 84.70 % 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 are not related in a simple way. whole: -0.71 (0.26), residues: 1062 helix: -2.59 (0.66), residues: 45 sheet: 0.60 (0.23), residues: 558 loop : -1.64 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 328 TYR 0.008 0.001 TYR A 236 PHE 0.010 0.001 PHE A 325 TRP 0.008 0.001 TRP B 337 HIS 0.002 0.000 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7684) covalent geometry : angle 0.49087 / 0.28 (10414) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.41125 / 0.22 ( 2) hydrogen bonds : bond 0.03981 / 2.74 ( 416) hydrogen bonds : angle 4.71146 / 3.19 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.284 Fit side-chains REVERT: A 37 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7956 (tmtt) REVERT: A 235 ASP cc_start: 0.8319 (t0) cc_final: 0.8047 (t0) REVERT: A 322 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7956 (t0) REVERT: B 196 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7501 (tttt) REVERT: B 235 ASP cc_start: 0.8117 (t0) cc_final: 0.7726 (t0) REVERT: B 263 ASN cc_start: 0.8176 (t0) cc_final: 0.7788 (t0) REVERT: C 124 ASN cc_start: 0.9270 (m-40) cc_final: 0.8965 (m-40) outliers start: 16 outliers final: 11 residues processed: 59 average time/residue: 0.0594 time to fit residues: 5.4471 Evaluate side-chains 54 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [84, 90, 91, 26, 22, 64, 103, 80, 20, 52, 85] chunk 84 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135019 restraints weight = 8152.849| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.21 r_work: 0.3509 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7685 Z= 0.172 Angle : 0.546 5.226 10416 Z= 0.315 Chirality : 0.044 0.147 1128 Planarity : 0.003 0.049 1373 Dihedral : 4.137 18.723 1167 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.06 % Allowed : 13.20 % Favored : 83.74 % 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 are not related in a simple way. whole: -0.74 (0.26), residues: 1062 helix: -2.66 (0.65), residues: 45 sheet: 0.54 (0.23), residues: 564 loop : -1.62 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.012 0.001 TYR C 312 PHE 0.019 0.001 PHE A 325 TRP 0.011 0.001 TRP C 337 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7684) covalent geometry : angle 0.54635 / 0.31 (10414) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.72685 / 0.39 ( 2) hydrogen bonds : bond 0.04923 / 3.37 ( 416) hydrogen bonds : angle 4.79647 / 3.24 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7989 (tmtt) REVERT: A 235 ASP cc_start: 0.8370 (t0) cc_final: 0.8148 (t0) REVERT: A 322 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7978 (t0) REVERT: B 235 ASP cc_start: 0.8256 (t0) cc_final: 0.7942 (t0) REVERT: B 263 ASN cc_start: 0.8260 (t0) cc_final: 0.7887 (t0) REVERT: C 124 ASN cc_start: 0.9286 (m-40) cc_final: 0.8977 (m-40) outliers start: 19 outliers final: 15 residues processed: 58 average time/residue: 0.0578 time to fit residues: 5.1639 Evaluate side-chains 57 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [98, 70, 99, 49, 65, 35, 15, 105, 85, 83, 57] chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136778 restraints weight = 8198.886| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.24 r_work: 0.3514 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7685 Z= 0.139 Angle : 0.518 5.147 10416 Z= 0.298 Chirality : 0.044 0.143 1128 Planarity : 0.003 0.048 1373 Dihedral : 4.064 18.854 1167 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.90 % Allowed : 13.69 % Favored : 83.41 % 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 are not related in a simple way. whole: -0.67 (0.26), residues: 1062 helix: -2.64 (0.65), residues: 45 sheet: 0.63 (0.23), residues: 558 loop : -1.61 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 145 TYR 0.010 0.001 TYR C 312 PHE 0.015 0.001 PHE A 325 TRP 0.010 0.001 TRP C 337 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7684) covalent geometry : angle 0.51793 / 0.30 (10414) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.58985 / 0.31 ( 2) hydrogen bonds : bond 0.04514 / 3.10 ( 416) hydrogen bonds : angle 4.75500 / 3.22 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8016 (tmtt) REVERT: A 235 ASP cc_start: 0.8277 (t0) cc_final: 0.8053 (t0) REVERT: A 322 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7831 (t0) REVERT: B 235 ASP cc_start: 0.8118 (t0) cc_final: 0.7778 (t0) REVERT: C 124 ASN cc_start: 0.9245 (m-40) cc_final: 0.8965 (m-40) outliers start: 18 outliers final: 15 residues processed: 57 average time/residue: 0.0612 time to fit residues: 5.4576 Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [100, 34, 90, 104, 28, 56, 14, 67, 80, 51, 74] chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135673 restraints weight = 8185.317| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.25 r_work: 0.3500 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7685 Z= 0.161 Angle : 0.539 5.317 10416 Z= 0.310 Chirality : 0.044 0.143 1128 Planarity : 0.003 0.049 1373 Dihedral : 4.122 18.757 1167 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.06 % Allowed : 13.69 % Favored : 83.25 % 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 are not related in a simple way. whole: -0.70 (0.26), residues: 1062 helix: -2.68 (0.64), residues: 45 sheet: 0.60 (0.23), residues: 558 loop : -1.60 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 154 TYR 0.011 0.001 TYR C 312 PHE 0.017 0.001 PHE A 325 TRP 0.010 0.001 TRP C 337 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7684) covalent geometry : angle 0.53851 / 0.31 (10414) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.71741 / 0.38 ( 2) hydrogen bonds : bond 0.04806 / 3.29 ( 416) hydrogen bonds : angle 4.78224 / 3.24 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (tmtt) REVERT: A 196 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7755 (tppt) REVERT: A 235 ASP cc_start: 0.8391 (t0) cc_final: 0.8180 (t0) REVERT: A 322 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8038 (t0) REVERT: B 235 ASP cc_start: 0.8241 (t0) cc_final: 0.7959 (t0) REVERT: C 124 ASN cc_start: 0.9257 (m-40) cc_final: 0.8992 (m-40) outliers start: 19 outliers final: 16 residues processed: 57 average time/residue: 0.0626 time to fit residues: 5.7039 Evaluate side-chains 57 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [74, 100, 73, 38, 90, 57, 27, 42, 97, 96, 65] chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135127 restraints weight = 8181.188| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.25 r_work: 0.3505 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7685 Z= 0.173 Angle : 0.552 5.374 10416 Z= 0.318 Chirality : 0.044 0.144 1128 Planarity : 0.003 0.049 1373 Dihedral : 4.207 18.818 1167 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.22 % Allowed : 13.37 % Favored : 83.41 % 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 are not related in a simple way. whole: -0.72 (0.26), residues: 1062 helix: -2.70 (0.64), residues: 45 sheet: 0.65 (0.23), residues: 552 loop : -1.68 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.012 0.001 TYR C 312 PHE 0.018 0.001 PHE A 325 TRP 0.011 0.001 TRP C 337 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 7684) covalent geometry : angle 0.55200 / 0.32 (10414) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 0.79350 / 0.42 ( 2) hydrogen bonds : bond 0.04986 / 3.42 ( 416) hydrogen bonds : angle 4.82181 / 3.27 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7997 (tmtt) REVERT: A 196 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7620 (tppt) REVERT: A 235 ASP cc_start: 0.8354 (t0) cc_final: 0.8118 (t0) REVERT: A 322 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7990 (t0) REVERT: B 235 ASP cc_start: 0.8238 (t0) cc_final: 0.7964 (t0) REVERT: C 124 ASN cc_start: 0.9267 (m-40) cc_final: 0.8973 (m-40) outliers start: 20 outliers final: 18 residues processed: 57 average time/residue: 0.0524 time to fit residues: 4.8150 Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [82, 56, 96, 11, 89, 1, 58, 24, 69, 80, 105] chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 263 ASN B 298 HIS B 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129853 restraints weight = 8364.395| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.28 r_work: 0.3439 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 7685 Z= 0.346 Angle : 0.725 6.133 10416 Z= 0.417 Chirality : 0.048 0.163 1128 Planarity : 0.004 0.053 1373 Dihedral : 4.886 18.397 1167 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.22 % Allowed : 13.37 % Favored : 83.41 % 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 are not related in a simple way. whole: -1.24 (0.26), residues: 1062 helix: -2.89 (0.62), residues: 45 sheet: 0.26 (0.23), residues: 552 loop : -1.99 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 154 TYR 0.020 0.003 TYR C 312 PHE 0.028 0.002 PHE A 325 TRP 0.018 0.002 TRP A 337 HIS 0.004 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.35 ( 7684) covalent geometry : angle 0.72443 / 0.42 (10414) SS BOND : bond 0.00268 / 0.14 ( 1) SS BOND : angle 1.63179 / 0.86 ( 2) hydrogen bonds : bond 0.06907 / 4.71 ( 416) hydrogen bonds : angle 5.15056 / 3.49 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.64 seconds wall clock time: 28 minutes 23.57 seconds (1703.57 seconds total)