Starting phenix.real_space_refine on Sat Aug 3 11:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4o_36888/08_2024/8k4o_36888.cif" } resolution = 3.01 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= -0.002 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5054 2.51 5 N 1369 2.21 5 O 1463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 121": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7946 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2664 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 7, 'TRANS': 325} Chain: "F" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2572 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1825 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 226} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Time building chain proxies: 5.39, per 1000 atoms: 0.68 Number of scatterers: 7946 At special positions: 0 Unit cell: (74.8, 102.85, 164.9, 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 60 16.00 O 1463 8.00 N 1369 7.00 C 5054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 118 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 35 " distance=2.03 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'E' and resid 46 through 75 removed outlier: 3.792A pdb=" N ASN E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.951A pdb=" N ILE E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER E 99 " --> pdb=" O CYS E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 110 through 113 removed outlier: 3.807A pdb=" N ILE E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 114 through 149 removed outlier: 3.599A pdb=" N ARG E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 Processing helix chain 'E' and resid 157 through 180 removed outlier: 3.919A pdb=" N GLY E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 4.136A pdb=" N MET E 203 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 204 " --> pdb=" O GLY E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 204' Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.649A pdb=" N ARG E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 239 removed outlier: 3.615A pdb=" N THR E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 279 removed outlier: 3.617A pdb=" N ALA E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Proline residue: E 266 - end of helix removed outlier: 3.548A pdb=" N ASN E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 272 " --> pdb=" O HIS E 268 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 309 removed outlier: 3.824A pdb=" N ALA E 297 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 317 removed outlier: 3.577A pdb=" N LEU E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.770A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.742A pdb=" N ILE F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.766A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'C' and resid 9 through 12 Processing helix chain 'C' and resid 13 through 30 removed outlier: 3.611A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.681A pdb=" N LYS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.652A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.790A pdb=" N ASN C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.523A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.715A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.574A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'E' and resid 183 through 187 Processing sheet with id=AA2, first strand: chain 'F' and resid 25 through 28 removed outlier: 3.594A pdb=" N LEU F 44 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.862A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.624A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.908A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.600A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.012A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.605A pdb=" N ASP C 200 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 190 removed outlier: 6.147A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 936 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: 2.27 Time building geometry restraints manager: 3.37 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: 2581 1.34 - 1.46: 1354 1.46 - 1.58: 4079 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8096 Sorted by residual: bond pdb=" CA ARG E 283 " pdb=" C ARG E 283 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.32e-02 5.74e+03 1.65e+01 bond pdb=" C THR G 52 " pdb=" O THR G 52 " ideal model delta sigma weight residual 1.246 1.229 0.017 9.20e-03 1.18e+04 3.51e+00 bond pdb=" CA LEU G 50 " pdb=" C LEU G 50 " ideal model delta sigma weight residual 1.523 1.501 0.023 1.34e-02 5.57e+03 2.82e+00 bond pdb=" CA LEU G 51 " pdb=" C LEU G 51 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.30e-02 5.92e+03 1.60e+00 bond pdb=" C SER F 56 " pdb=" N PRO F 57 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.48e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.93: 110 105.93 - 112.94: 4447 112.94 - 119.96: 2727 119.96 - 126.98: 3595 126.98 - 133.99: 86 Bond angle restraints: 10965 Sorted by residual: angle pdb=" C CYS C 325 " pdb=" CA CYS C 325 " pdb=" CB CYS C 325 " ideal model delta sigma weight residual 116.54 109.59 6.95 1.15e+00 7.56e-01 3.65e+01 angle pdb=" N LEU G 51 " pdb=" CA LEU G 51 " pdb=" C LEU G 51 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N VAL E 147 " pdb=" CA VAL E 147 " pdb=" C VAL E 147 " ideal model delta sigma weight residual 112.96 108.53 4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA CYS C 325 " pdb=" C CYS C 325 " pdb=" N ALA C 326 " ideal model delta sigma weight residual 119.52 116.56 2.96 7.90e-01 1.60e+00 1.41e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" C PRO G 60 " ideal model delta sigma weight residual 113.65 109.22 4.43 1.35e+00 5.49e-01 1.07e+01 ... (remaining 10960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4073 17.32 - 34.64: 565 34.64 - 51.96: 163 51.96 - 69.28: 38 69.28 - 86.60: 5 Dihedral angle restraints: 4844 sinusoidal: 1889 harmonic: 2955 Sorted by residual: dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP E 207 " pdb=" C TRP E 207 " pdb=" N ARG E 208 " pdb=" CA ARG E 208 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP C 237 " pdb=" C ASP C 237 " pdb=" N GLU C 238 " pdb=" CA GLU C 238 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 711 0.026 - 0.052: 338 0.052 - 0.078: 133 0.078 - 0.104: 51 0.104 - 0.129: 38 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CB THR B 87 " pdb=" CA THR B 87 " pdb=" OG1 THR B 87 " pdb=" CG2 THR B 87 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1268 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 32 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO F 33 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 33 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 33 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 163 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" CG ASP B 163 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP B 163 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 163 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 281 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 282 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 282 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 282 " -0.025 5.00e-02 4.00e+02 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 347 2.72 - 3.26: 7629 3.26 - 3.81: 11975 3.81 - 4.35: 15035 4.35 - 4.90: 26647 Nonbonded interactions: 61633 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.252 3.040 nonbonded pdb=" O GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.269 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.274 3.040 nonbonded pdb=" N ASP B 186 " pdb=" OD1 ASP B 186 " model vdw 2.277 3.120 ... (remaining 61628 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: 1.500 Set stop_for_unknowns flag: 0.010 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 : 0.003 0.054 8096 Z= 0.181 Angle : 0.585 8.836 10965 Z= 0.334 Chirality : 0.040 0.129 1271 Planarity : 0.004 0.088 1382 Dihedral : 17.481 86.602 2921 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.21 % Allowed : 30.26 % Favored : 63.52 % 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: -1.17 (0.26), residues: 1002 helix: 0.33 (0.27), residues: 393 sheet: -0.33 (0.36), residues: 184 loop : -2.05 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.012 0.001 PHE B 241 TYR 0.009 0.001 TYR E 128 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 103 time to evaluate : 0.889 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: C 273 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (tt) outliers start: 54 outliers final: 52 residues processed: 155 average time/residue: 0.1894 time to fit residues: 40.3070 Evaluate side-chains 156 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 103 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8096 Z= 0.289 Angle : 0.583 6.085 10965 Z= 0.314 Chirality : 0.043 0.140 1271 Planarity : 0.004 0.068 1382 Dihedral : 9.214 74.508 1177 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.33 % Allowed : 27.96 % Favored : 65.71 % 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: -1.18 (0.26), residues: 1002 helix: 0.42 (0.28), residues: 389 sheet: -0.35 (0.37), residues: 182 loop : -2.14 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.002 PHE B 241 TYR 0.014 0.001 TYR E 128 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 110 time to evaluate : 0.961 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 21 LEU cc_start: 0.4305 (OUTLIER) cc_final: 0.4100 (mm) REVERT: E 182 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8462 (m170) REVERT: E 289 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7546 (ptt180) REVERT: B 163 ASP cc_start: 0.7549 (t0) cc_final: 0.7328 (t0) REVERT: C 23 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7392 (mp) REVERT: C 26 ASP cc_start: 0.8250 (m-30) cc_final: 0.7978 (m-30) REVERT: C 33 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: C 273 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8412 (tt) REVERT: G 9 ILE cc_start: 0.4646 (OUTLIER) cc_final: 0.4242 (pp) outliers start: 55 outliers final: 32 residues processed: 156 average time/residue: 0.2131 time to fit residues: 45.3569 Evaluate side-chains 138 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.0000 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8096 Z= 0.213 Angle : 0.534 5.456 10965 Z= 0.288 Chirality : 0.041 0.135 1271 Planarity : 0.004 0.060 1382 Dihedral : 8.171 75.992 1141 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.41 % Allowed : 28.65 % Favored : 65.94 % 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: -1.03 (0.26), residues: 1002 helix: 0.61 (0.28), residues: 390 sheet: -0.25 (0.37), residues: 179 loop : -2.13 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS C 213 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR E 128 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 108 time to evaluate : 0.929 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 21 LEU cc_start: 0.4551 (OUTLIER) cc_final: 0.4334 (mm) REVERT: E 70 TYR cc_start: 0.8352 (t80) cc_final: 0.8031 (t80) REVERT: B 22 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6983 (ttm-80) REVERT: B 57 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8705 (mttt) REVERT: B 163 ASP cc_start: 0.7441 (t0) cc_final: 0.7217 (t0) REVERT: B 323 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8091 (p0) REVERT: C 26 ASP cc_start: 0.8239 (m-30) cc_final: 0.7962 (m-30) REVERT: C 33 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: C 273 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8404 (tt) REVERT: G 9 ILE cc_start: 0.4581 (OUTLIER) cc_final: 0.4129 (pp) outliers start: 47 outliers final: 30 residues processed: 147 average time/residue: 0.1919 time to fit residues: 38.3084 Evaluate side-chains 137 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8096 Z= 0.336 Angle : 0.585 6.013 10965 Z= 0.315 Chirality : 0.043 0.140 1271 Planarity : 0.004 0.059 1382 Dihedral : 7.964 81.144 1133 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.79 % Allowed : 27.27 % Favored : 65.94 % 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: -1.17 (0.26), residues: 1002 helix: 0.49 (0.28), residues: 391 sheet: -0.45 (0.36), residues: 181 loop : -2.15 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS C 213 PHE 0.016 0.002 PHE B 241 TYR 0.016 0.001 TYR B 111 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 111 time to evaluate : 0.947 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 21 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4177 (mm) REVERT: E 61 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8466 (t0) REVERT: E 289 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7634 (ptt180) REVERT: B 22 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7049 (ttm-80) REVERT: B 57 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8736 (mttt) REVERT: B 66 ASP cc_start: 0.8259 (p0) cc_final: 0.8034 (p0) REVERT: B 314 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8332 (mtt180) REVERT: C 23 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7462 (mp) REVERT: C 26 ASP cc_start: 0.8253 (m-30) cc_final: 0.7957 (m-30) REVERT: C 33 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: C 273 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8371 (tt) REVERT: G 9 ILE cc_start: 0.4693 (OUTLIER) cc_final: 0.4273 (pp) outliers start: 59 outliers final: 38 residues processed: 160 average time/residue: 0.2040 time to fit residues: 44.0347 Evaluate side-chains 150 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 102 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 81 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8096 Z= 0.173 Angle : 0.513 5.385 10965 Z= 0.279 Chirality : 0.041 0.132 1271 Planarity : 0.004 0.053 1382 Dihedral : 7.520 79.500 1129 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.18 % Allowed : 28.54 % Favored : 66.28 % 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: -0.95 (0.26), residues: 1002 helix: 0.72 (0.28), residues: 391 sheet: -0.31 (0.37), residues: 179 loop : -2.09 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS C 213 PHE 0.010 0.001 PHE C 189 TYR 0.010 0.001 TYR E 128 ARG 0.003 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 109 time to evaluate : 0.934 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.3856 (pt0) REVERT: E 21 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4229 (mm) REVERT: E 70 TYR cc_start: 0.8370 (t80) cc_final: 0.8046 (t80) REVERT: B 314 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8209 (mtt180) REVERT: C 33 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: C 231 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: C 273 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8377 (tt) REVERT: G 9 ILE cc_start: 0.4686 (OUTLIER) cc_final: 0.4249 (pp) outliers start: 45 outliers final: 29 residues processed: 146 average time/residue: 0.2053 time to fit residues: 40.3121 Evaluate side-chains 137 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8096 Z= 0.273 Angle : 0.585 16.256 10965 Z= 0.305 Chirality : 0.043 0.236 1271 Planarity : 0.004 0.052 1382 Dihedral : 7.517 82.166 1129 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.87 % Allowed : 28.08 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1002 helix: 0.67 (0.28), residues: 391 sheet: -0.42 (0.36), residues: 181 loop : -2.10 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS C 213 PHE 0.014 0.002 PHE B 241 TYR 0.014 0.001 TYR B 111 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 103 time to evaluate : 0.952 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4898 (OUTLIER) cc_final: 0.3957 (pt0) REVERT: E 289 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7311 (ptp-170) REVERT: B 22 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.7067 (ttm-80) REVERT: B 57 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8691 (mttt) REVERT: B 66 ASP cc_start: 0.8158 (p0) cc_final: 0.7949 (p0) REVERT: B 163 ASP cc_start: 0.7509 (t0) cc_final: 0.7300 (t0) REVERT: B 314 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8320 (mtt180) REVERT: C 23 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7446 (mp) REVERT: C 33 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: C 273 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8377 (tt) REVERT: G 9 ILE cc_start: 0.4684 (OUTLIER) cc_final: 0.4252 (pp) outliers start: 51 outliers final: 38 residues processed: 147 average time/residue: 0.2187 time to fit residues: 42.7033 Evaluate side-chains 146 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8096 Z= 0.185 Angle : 0.536 14.762 10965 Z= 0.281 Chirality : 0.041 0.225 1271 Planarity : 0.003 0.050 1382 Dihedral : 7.273 81.347 1129 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.75 % Allowed : 28.54 % Favored : 65.71 % 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: -0.90 (0.26), residues: 1002 helix: 0.79 (0.28), residues: 394 sheet: -0.28 (0.37), residues: 179 loop : -2.10 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS C 213 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR E 128 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 0.876 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.3936 (pt0) REVERT: E 70 TYR cc_start: 0.8385 (t80) cc_final: 0.8071 (t80) REVERT: E 207 TRP cc_start: 0.8512 (t-100) cc_final: 0.8302 (t-100) REVERT: B 57 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8685 (mttt) REVERT: B 314 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8272 (mtt180) REVERT: C 17 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7116 (mtpm) REVERT: C 23 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7425 (mp) REVERT: C 33 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 273 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8382 (tt) REVERT: G 9 ILE cc_start: 0.4533 (OUTLIER) cc_final: 0.4091 (pp) outliers start: 50 outliers final: 36 residues processed: 151 average time/residue: 0.2090 time to fit residues: 42.0972 Evaluate side-chains 144 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 18 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8096 Z= 0.126 Angle : 0.513 15.364 10965 Z= 0.266 Chirality : 0.040 0.222 1271 Planarity : 0.003 0.048 1382 Dihedral : 6.944 77.901 1127 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.26 % Allowed : 29.92 % Favored : 65.82 % 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: -0.65 (0.27), residues: 1002 helix: 1.07 (0.29), residues: 391 sheet: -0.24 (0.38), residues: 172 loop : -1.96 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS E 210 PHE 0.010 0.001 PHE E 107 TYR 0.009 0.001 TYR C 290 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 0.838 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4867 (OUTLIER) cc_final: 0.3861 (pt0) REVERT: E 70 TYR cc_start: 0.8371 (t80) cc_final: 0.8072 (t80) REVERT: B 17 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 57 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8642 (mttt) REVERT: B 314 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8169 (mtt180) REVERT: C 17 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7107 (mtmm) REVERT: C 23 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7425 (mp) REVERT: C 33 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: C 273 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8403 (tt) REVERT: G 9 ILE cc_start: 0.4727 (OUTLIER) cc_final: 0.4255 (pp) outliers start: 37 outliers final: 28 residues processed: 143 average time/residue: 0.2090 time to fit residues: 40.1182 Evaluate side-chains 142 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 0.0060 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8096 Z= 0.154 Angle : 0.535 16.230 10965 Z= 0.277 Chirality : 0.041 0.214 1271 Planarity : 0.003 0.047 1382 Dihedral : 6.895 79.346 1126 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.26 % Allowed : 30.15 % Favored : 65.59 % 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: -0.63 (0.27), residues: 1002 helix: 1.06 (0.29), residues: 394 sheet: -0.20 (0.39), residues: 172 loop : -1.96 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS E 268 PHE 0.014 0.001 PHE E 107 TYR 0.009 0.001 TYR C 287 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.3839 (pt0) REVERT: E 70 TYR cc_start: 0.8368 (t80) cc_final: 0.8073 (t80) REVERT: B 17 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 57 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8650 (mttt) REVERT: B 314 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8277 (mtt180) REVERT: C 23 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7457 (mp) REVERT: C 33 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6989 (mm-30) REVERT: C 273 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8405 (tt) REVERT: G 9 ILE cc_start: 0.4792 (OUTLIER) cc_final: 0.4315 (pp) outliers start: 37 outliers final: 29 residues processed: 140 average time/residue: 0.2125 time to fit residues: 39.8739 Evaluate side-chains 140 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 0.0040 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8096 Z= 0.139 Angle : 0.525 16.117 10965 Z= 0.272 Chirality : 0.041 0.215 1271 Planarity : 0.003 0.047 1382 Dihedral : 6.650 78.614 1124 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.26 % Allowed : 30.15 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 1002 helix: 1.21 (0.29), residues: 391 sheet: -0.14 (0.39), residues: 172 loop : -1.93 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.011 0.001 PHE E 107 TYR 0.009 0.001 TYR C 290 ARG 0.007 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.3891 (pt0) REVERT: E 70 TYR cc_start: 0.8360 (t80) cc_final: 0.8070 (t80) REVERT: B 57 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8644 (mttt) REVERT: B 314 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8172 (mtt180) REVERT: C 23 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 33 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: C 273 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8391 (tt) REVERT: G 9 ILE cc_start: 0.4712 (OUTLIER) cc_final: 0.4252 (pp) outliers start: 37 outliers final: 30 residues processed: 138 average time/residue: 0.2095 time to fit residues: 38.5553 Evaluate side-chains 139 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 102 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 80 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.157458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108253 restraints weight = 9392.765| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.72 r_work: 0.3080 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8096 Z= 0.167 Angle : 0.540 16.472 10965 Z= 0.280 Chirality : 0.041 0.208 1271 Planarity : 0.003 0.047 1382 Dihedral : 6.654 79.503 1122 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.60 % Allowed : 29.57 % Favored : 65.82 % 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: -0.56 (0.27), residues: 1002 helix: 1.11 (0.29), residues: 394 sheet: -0.14 (0.39), residues: 172 loop : -1.91 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS E 268 PHE 0.012 0.001 PHE E 107 TYR 0.013 0.001 TYR C 287 ARG 0.007 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.67 seconds wall clock time: 38 minutes 49.44 seconds (2329.44 seconds total)