Starting phenix.real_space_refine on Wed Sep 17 12:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8z_61249/09_2025/9j8z_61249.cif" } resolution = 3.36 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5450 2.51 5 N 1479 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8611 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2050 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 88 Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8611 At special positions: 0 Unit cell: (87.15, 122.84, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1620 8.00 N 1479 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 165 " 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: 0.73 Conformation dependent library (CDL) restraints added in 423.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 36.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.941A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.686A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.384A pdb=" N GLN C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.989A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.030A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.598A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.587A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.926A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 43 removed outlier: 3.766A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.660A pdb=" N ARG A 71 " --> pdb=" O CYS A 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 128 through 152 removed outlier: 4.528A pdb=" N TYR A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 205 removed outlier: 3.893A pdb=" N PHE A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.968A pdb=" N ARG A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 212 " --> pdb=" O LEU A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 213 through 245 removed outlier: 3.648A pdb=" N ALA A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 255 through 282 removed outlier: 6.852A pdb=" N HIS A 261 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 4.022A pdb=" N PHE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.750A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.784A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.839A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.720A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.675A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.785A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.643A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.802A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.802A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.734A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1128 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: 1.38 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1418 1.32 - 1.44: 2445 1.44 - 1.57: 4844 1.57 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 8794 Sorted by residual: bond pdb=" C ILE A 169 " pdb=" O ILE A 169 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" CA ASP A 73 " pdb=" C ASP A 73 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.39e-02 5.18e+03 9.89e+00 bond pdb=" N ILE A 169 " pdb=" CA ILE A 169 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.25e-02 6.40e+03 6.65e+00 bond pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 1.459 1.431 0.027 1.16e-02 7.43e+03 5.58e+00 bond pdb=" CA GLU A 171 " pdb=" C GLU A 171 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.34e-02 5.57e+03 5.16e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11691 2.46 - 4.93: 185 4.93 - 7.39: 42 7.39 - 9.86: 9 9.86 - 12.32: 2 Bond angle restraints: 11929 Sorted by residual: angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 111.28 121.01 -9.73 1.09e+00 8.42e-01 7.97e+01 angle pdb=" N ILE A 14 " pdb=" CA ILE A 14 " pdb=" C ILE A 14 " ideal model delta sigma weight residual 111.81 104.25 7.56 8.60e-01 1.35e+00 7.72e+01 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" C ILE A 9 " ideal model delta sigma weight residual 108.93 97.68 11.25 1.35e+00 5.49e-01 6.94e+01 angle pdb=" N MET A 180 " pdb=" CA MET A 180 " pdb=" C MET A 180 " ideal model delta sigma weight residual 111.14 102.59 8.55 1.08e+00 8.57e-01 6.26e+01 angle pdb=" C ILE A 14 " pdb=" CA ILE A 14 " pdb=" CB ILE A 14 " ideal model delta sigma weight residual 111.55 104.55 7.00 1.15e+00 7.56e-01 3.71e+01 ... (remaining 11924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4406 17.20 - 34.40: 606 34.40 - 51.60: 162 51.60 - 68.81: 23 68.81 - 86.01: 14 Dihedral angle restraints: 5211 sinusoidal: 1964 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 165 " pdb=" CB CYS A 165 " ideal model delta sinusoidal sigma weight residual -86.00 -161.82 75.82 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CA LYS G 20 " pdb=" C LYS G 20 " pdb=" N MET G 21 " pdb=" CA MET G 21 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PHE C 323 " pdb=" C PHE C 323 " pdb=" N THR C 324 " pdb=" CA THR C 324 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1216 0.075 - 0.151: 126 0.151 - 0.226: 4 0.226 - 0.302: 4 0.302 - 0.377: 2 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA ILE A 14 " pdb=" N ILE A 14 " pdb=" C ILE A 14 " pdb=" CB ILE A 14 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA LEU B 55 " pdb=" N LEU B 55 " pdb=" C LEU B 55 " pdb=" CB LEU B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA SER A 172 " pdb=" N SER A 172 " pdb=" C SER A 172 " pdb=" CB SER A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1349 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 86 " 0.091 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO A 87 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 135 " 0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO S 136 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO S 136 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO S 136 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 72 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C THR A 72 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 72 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 73 " -0.019 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 299 2.68 - 3.24: 8591 3.24 - 3.79: 13471 3.79 - 4.35: 16964 4.35 - 4.90: 28499 Nonbonded interactions: 67824 Sorted by model distance: nonbonded pdb=" OG1 THR C 295 " pdb=" OE1 GLU C 298 " model vdw 2.128 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.168 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 50 " pdb=" OD2 ASP A 112 " model vdw 2.223 3.040 ... (remaining 67819 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8799 Z= 0.205 Angle : 0.794 12.321 11939 Z= 0.469 Chirality : 0.047 0.377 1352 Planarity : 0.006 0.141 1522 Dihedral : 17.033 86.008 3100 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.42 % Allowed : 30.20 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.26), residues: 1105 helix: 0.89 (0.28), residues: 377 sheet: -0.31 (0.33), residues: 271 loop : -1.09 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 19 TYR 0.012 0.001 TYR A 268 PHE 0.010 0.001 PHE A 168 TRP 0.025 0.001 TRP S 47 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8794) covalent geometry : angle 0.79365 (11929) SS BOND : bond 0.00258 ( 5) SS BOND : angle 1.47478 ( 10) hydrogen bonds : bond 0.17056 ( 399) hydrogen bonds : angle 7.34124 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.8441 (mtp) cc_final: 0.8108 (mtp) REVERT: B 262 MET cc_start: 0.8668 (mmm) cc_final: 0.8409 (mmm) REVERT: C 243 MET cc_start: 0.9218 (tpp) cc_final: 0.8328 (mpp) REVERT: C 346 ASN cc_start: 0.8541 (m110) cc_final: 0.8162 (m110) REVERT: S 189 ASP cc_start: 0.8768 (t0) cc_final: 0.8511 (p0) REVERT: S 234 GLU cc_start: 0.8350 (pm20) cc_final: 0.7865 (pm20) outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 0.1051 time to fit residues: 22.6959 Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072771 restraints weight = 18375.728| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.82 r_work: 0.2943 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8799 Z= 0.123 Angle : 0.582 7.208 11939 Z= 0.308 Chirality : 0.042 0.140 1352 Planarity : 0.005 0.065 1522 Dihedral : 5.318 54.752 1224 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.27 % Allowed : 27.13 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 1105 helix: 1.52 (0.28), residues: 373 sheet: 0.03 (0.33), residues: 268 loop : -1.03 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.016 0.001 TYR S 178 PHE 0.024 0.001 PHE A 168 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8794) covalent geometry : angle 0.58198 (11929) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.59829 ( 10) hydrogen bonds : bond 0.03971 ( 399) hydrogen bonds : angle 5.11365 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: B 217 MET cc_start: 0.7587 (ppp) cc_final: 0.7322 (ppp) REVERT: B 254 ASP cc_start: 0.8719 (t70) cc_final: 0.8327 (t0) REVERT: B 262 MET cc_start: 0.8917 (mmm) cc_final: 0.8628 (mmm) REVERT: C 20 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: C 53 MET cc_start: 0.4327 (OUTLIER) cc_final: 0.3864 (ttt) REVERT: C 243 MET cc_start: 0.9345 (tpp) cc_final: 0.8859 (mpp) REVERT: C 280 LYS cc_start: 0.9288 (tppt) cc_final: 0.8998 (tmmt) REVERT: C 346 ASN cc_start: 0.8793 (m110) cc_final: 0.8376 (m110) REVERT: G 48 ASP cc_start: 0.8594 (t0) cc_final: 0.7549 (t0) REVERT: S 73 ASP cc_start: 0.8233 (t0) cc_final: 0.7801 (t0) REVERT: S 115 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8982 (p) REVERT: S 171 GLN cc_start: 0.8764 (pm20) cc_final: 0.8554 (pm20) REVERT: S 180 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (ptm) REVERT: S 189 ASP cc_start: 0.8940 (t70) cc_final: 0.8685 (p0) REVERT: S 232 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8519 (tmtt) REVERT: S 234 GLU cc_start: 0.8373 (pm20) cc_final: 0.7611 (pm20) REVERT: A 71 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7768 (mmm160) REVERT: A 233 TYR cc_start: 0.6885 (m-80) cc_final: 0.6462 (m-80) outliers start: 39 outliers final: 22 residues processed: 187 average time/residue: 0.0946 time to fit residues: 24.2416 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.105089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.075346 restraints weight = 18653.569| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.88 r_work: 0.3064 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8799 Z= 0.119 Angle : 0.549 7.034 11939 Z= 0.289 Chirality : 0.041 0.142 1352 Planarity : 0.004 0.054 1522 Dihedral : 5.201 57.323 1223 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.69 % Allowed : 25.27 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1105 helix: 1.78 (0.28), residues: 367 sheet: 0.13 (0.33), residues: 270 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.028 0.001 PHE A 168 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8794) covalent geometry : angle 0.54870 (11929) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.55010 ( 10) hydrogen bonds : bond 0.03463 ( 399) hydrogen bonds : angle 4.64355 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 217 MET cc_start: 0.7795 (ppp) cc_final: 0.7513 (ppp) REVERT: B 254 ASP cc_start: 0.8870 (t70) cc_final: 0.8565 (t0) REVERT: B 262 MET cc_start: 0.9088 (mmm) cc_final: 0.8786 (mmm) REVERT: C 20 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: C 53 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.4176 (ttt) REVERT: C 243 MET cc_start: 0.9370 (tpp) cc_final: 0.8816 (mpp) REVERT: C 298 GLU cc_start: 0.9051 (mp0) cc_final: 0.8659 (mp0) REVERT: C 331 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: C 346 ASN cc_start: 0.8931 (m110) cc_final: 0.8456 (m110) REVERT: G 48 ASP cc_start: 0.8683 (t0) cc_final: 0.7635 (t0) REVERT: S 43 LYS cc_start: 0.9330 (mmtm) cc_final: 0.9120 (mmtm) REVERT: S 73 ASP cc_start: 0.8503 (t0) cc_final: 0.8138 (t0) REVERT: S 115 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9056 (p) REVERT: S 171 GLN cc_start: 0.8852 (pm20) cc_final: 0.8612 (pm20) REVERT: S 180 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8983 (ptm) REVERT: S 189 ASP cc_start: 0.8889 (t70) cc_final: 0.8669 (p0) REVERT: S 210 GLU cc_start: 0.7911 (tp30) cc_final: 0.7690 (tp30) REVERT: S 222 GLU cc_start: 0.8627 (pm20) cc_final: 0.8401 (pm20) REVERT: S 232 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8396 (tmtt) REVERT: S 234 GLU cc_start: 0.8265 (pm20) cc_final: 0.7231 (pm20) REVERT: A 233 TYR cc_start: 0.7208 (m-80) cc_final: 0.6818 (m-80) outliers start: 52 outliers final: 35 residues processed: 197 average time/residue: 0.0826 time to fit residues: 22.7033 Evaluate side-chains 194 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.102019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072996 restraints weight = 18488.647| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.85 r_work: 0.2942 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8799 Z= 0.119 Angle : 0.542 6.480 11939 Z= 0.285 Chirality : 0.041 0.151 1352 Planarity : 0.004 0.052 1522 Dihedral : 4.670 47.571 1218 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.14 % Allowed : 26.26 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1105 helix: 1.79 (0.28), residues: 368 sheet: 0.13 (0.32), residues: 270 loop : -0.93 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.016 0.001 PHE A 168 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8794) covalent geometry : angle 0.54153 (11929) SS BOND : bond 0.00198 ( 5) SS BOND : angle 1.13778 ( 10) hydrogen bonds : bond 0.03274 ( 399) hydrogen bonds : angle 4.47608 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: B 217 MET cc_start: 0.7599 (ppp) cc_final: 0.7303 (ppp) REVERT: B 254 ASP cc_start: 0.8733 (t70) cc_final: 0.8372 (t0) REVERT: B 312 ASP cc_start: 0.9144 (t0) cc_final: 0.8732 (t0) REVERT: C 20 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8335 (m-30) REVERT: C 53 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.4030 (ttt) REVERT: C 243 MET cc_start: 0.9342 (tpp) cc_final: 0.8768 (mpp) REVERT: C 298 GLU cc_start: 0.9125 (mp0) cc_final: 0.8763 (mp0) REVERT: C 331 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: C 346 ASN cc_start: 0.8825 (m110) cc_final: 0.8352 (m110) REVERT: G 21 MET cc_start: 0.9043 (mmp) cc_final: 0.8841 (mmp) REVERT: G 46 LYS cc_start: 0.9454 (tppp) cc_final: 0.8920 (tppp) REVERT: G 48 ASP cc_start: 0.8588 (t0) cc_final: 0.7461 (t0) REVERT: S 73 ASP cc_start: 0.8381 (t0) cc_final: 0.8000 (t0) REVERT: S 115 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (p) REVERT: S 171 GLN cc_start: 0.8743 (pm20) cc_final: 0.8443 (pm20) REVERT: S 180 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8907 (ptm) REVERT: S 222 GLU cc_start: 0.8708 (pm20) cc_final: 0.8312 (pm20) REVERT: S 232 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8434 (tmtt) REVERT: S 234 GLU cc_start: 0.8323 (pm20) cc_final: 0.7281 (pm20) REVERT: A 180 MET cc_start: 0.7398 (tmm) cc_final: 0.6891 (tmm) outliers start: 47 outliers final: 31 residues processed: 196 average time/residue: 0.0815 time to fit residues: 22.4261 Evaluate side-chains 193 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070968 restraints weight = 18962.007| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.01 r_work: 0.2906 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8799 Z= 0.151 Angle : 0.558 6.614 11939 Z= 0.295 Chirality : 0.042 0.138 1352 Planarity : 0.004 0.052 1522 Dihedral : 4.528 47.197 1216 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.47 % Allowed : 27.13 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1105 helix: 1.79 (0.28), residues: 369 sheet: 0.17 (0.33), residues: 268 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.014 0.001 PHE A 168 TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8794) covalent geometry : angle 0.55763 (11929) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.91595 ( 10) hydrogen bonds : bond 0.03428 ( 399) hydrogen bonds : angle 4.48548 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 16 ASN cc_start: 0.9104 (p0) cc_final: 0.8758 (p0) REVERT: B 59 TYR cc_start: 0.8667 (m-80) cc_final: 0.8190 (m-80) REVERT: B 217 MET cc_start: 0.7585 (ppp) cc_final: 0.7284 (ppp) REVERT: B 254 ASP cc_start: 0.8745 (t70) cc_final: 0.8381 (t0) REVERT: B 262 MET cc_start: 0.9049 (mmm) cc_final: 0.8697 (mmm) REVERT: B 312 ASP cc_start: 0.9160 (t0) cc_final: 0.8766 (t0) REVERT: C 53 MET cc_start: 0.4389 (OUTLIER) cc_final: 0.3968 (ttt) REVERT: C 243 MET cc_start: 0.9333 (tpp) cc_final: 0.8764 (mpp) REVERT: C 294 ASN cc_start: 0.8025 (t0) cc_final: 0.7814 (t0) REVERT: C 331 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: C 346 ASN cc_start: 0.8851 (m110) cc_final: 0.8382 (m110) REVERT: G 46 LYS cc_start: 0.9453 (tppp) cc_final: 0.9021 (tppp) REVERT: G 47 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8835 (mp0) REVERT: G 48 ASP cc_start: 0.8600 (t0) cc_final: 0.7685 (t0) REVERT: S 73 ASP cc_start: 0.8359 (t0) cc_final: 0.7960 (t0) REVERT: S 115 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (p) REVERT: S 171 GLN cc_start: 0.8764 (pm20) cc_final: 0.8459 (pm20) REVERT: S 180 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8930 (ptm) REVERT: S 189 ASP cc_start: 0.8923 (t0) cc_final: 0.8692 (p0) REVERT: S 222 GLU cc_start: 0.8775 (pm20) cc_final: 0.8324 (pm20) REVERT: S 232 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8387 (tmtt) REVERT: S 234 GLU cc_start: 0.8293 (pm20) cc_final: 0.7126 (pm20) REVERT: A 180 MET cc_start: 0.7374 (tmm) cc_final: 0.6882 (tmm) outliers start: 50 outliers final: 38 residues processed: 190 average time/residue: 0.0906 time to fit residues: 23.9596 Evaluate side-chains 197 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072496 restraints weight = 18467.521| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.86 r_work: 0.2931 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8799 Z= 0.127 Angle : 0.549 6.314 11939 Z= 0.287 Chirality : 0.041 0.140 1352 Planarity : 0.004 0.052 1522 Dihedral : 4.478 45.660 1216 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.13 % Allowed : 27.13 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1105 helix: 1.90 (0.28), residues: 363 sheet: 0.14 (0.32), residues: 271 loop : -0.90 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.012 0.001 PHE A 168 TRP 0.014 0.001 TRP S 47 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8794) covalent geometry : angle 0.54920 (11929) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.73792 ( 10) hydrogen bonds : bond 0.03273 ( 399) hydrogen bonds : angle 4.39114 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: B 59 TYR cc_start: 0.8597 (m-80) cc_final: 0.8142 (m-80) REVERT: B 217 MET cc_start: 0.7549 (ppp) cc_final: 0.7253 (ppp) REVERT: B 254 ASP cc_start: 0.8732 (t70) cc_final: 0.8390 (t0) REVERT: B 262 MET cc_start: 0.9071 (mmm) cc_final: 0.8663 (mmm) REVERT: B 312 ASP cc_start: 0.9134 (t0) cc_final: 0.8750 (t0) REVERT: C 53 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.3920 (ttt) REVERT: C 243 MET cc_start: 0.9338 (tpp) cc_final: 0.9054 (tpp) REVERT: C 280 LYS cc_start: 0.9180 (tppt) cc_final: 0.8964 (tmmt) REVERT: C 294 ASN cc_start: 0.8051 (t0) cc_final: 0.7844 (t0) REVERT: C 298 GLU cc_start: 0.9128 (mp0) cc_final: 0.8868 (mp0) REVERT: C 331 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8054 (m-40) REVERT: C 346 ASN cc_start: 0.8849 (m110) cc_final: 0.8349 (m110) REVERT: G 46 LYS cc_start: 0.9452 (tppp) cc_final: 0.9006 (tppp) REVERT: G 47 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8824 (mp0) REVERT: G 48 ASP cc_start: 0.8591 (t0) cc_final: 0.7606 (t0) REVERT: S 43 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8943 (mmmm) REVERT: S 73 ASP cc_start: 0.8363 (t0) cc_final: 0.7971 (t0) REVERT: S 115 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8986 (p) REVERT: S 168 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8264 (mtt90) REVERT: S 171 GLN cc_start: 0.8754 (pm20) cc_final: 0.8474 (pm20) REVERT: S 180 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8923 (ptm) REVERT: S 210 GLU cc_start: 0.8161 (tp30) cc_final: 0.7082 (tp30) REVERT: S 222 GLU cc_start: 0.8793 (pm20) cc_final: 0.8336 (pm20) REVERT: S 232 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8218 (tmtt) REVERT: S 234 GLU cc_start: 0.8303 (pm20) cc_final: 0.7073 (pm20) REVERT: A 180 MET cc_start: 0.7318 (tmm) cc_final: 0.6845 (tmm) outliers start: 56 outliers final: 39 residues processed: 196 average time/residue: 0.0883 time to fit residues: 24.1480 Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 168 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075153 restraints weight = 18806.261| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.85 r_work: 0.3058 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8799 Z= 0.126 Angle : 0.580 7.882 11939 Z= 0.301 Chirality : 0.041 0.155 1352 Planarity : 0.004 0.052 1522 Dihedral : 4.260 44.201 1214 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.69 % Allowed : 27.68 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1105 helix: 1.89 (0.28), residues: 363 sheet: 0.15 (0.32), residues: 271 loop : -0.93 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 168 TRP 0.014 0.001 TRP S 47 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8794) covalent geometry : angle 0.57985 (11929) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.68541 ( 10) hydrogen bonds : bond 0.03204 ( 399) hydrogen bonds : angle 4.35391 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: B 59 TYR cc_start: 0.8687 (m-80) cc_final: 0.8395 (m-80) REVERT: B 217 MET cc_start: 0.7708 (ppp) cc_final: 0.7404 (ppp) REVERT: B 254 ASP cc_start: 0.8842 (t70) cc_final: 0.8547 (t0) REVERT: B 262 MET cc_start: 0.9104 (mmm) cc_final: 0.8894 (mmm) REVERT: B 273 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 312 ASP cc_start: 0.8996 (t0) cc_final: 0.8594 (t0) REVERT: C 53 MET cc_start: 0.4767 (OUTLIER) cc_final: 0.4232 (ttt) REVERT: C 243 MET cc_start: 0.9348 (tpp) cc_final: 0.9092 (tpp) REVERT: C 294 ASN cc_start: 0.8082 (t0) cc_final: 0.7835 (t0) REVERT: C 298 GLU cc_start: 0.9122 (mp0) cc_final: 0.8875 (mp0) REVERT: C 331 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: C 346 ASN cc_start: 0.8967 (m110) cc_final: 0.8440 (m110) REVERT: G 46 LYS cc_start: 0.9410 (tppp) cc_final: 0.8956 (tppp) REVERT: G 47 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8813 (mp0) REVERT: G 48 ASP cc_start: 0.8644 (t0) cc_final: 0.7676 (t0) REVERT: S 73 ASP cc_start: 0.8514 (t0) cc_final: 0.8168 (t0) REVERT: S 115 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9057 (p) REVERT: S 168 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8232 (mtt90) REVERT: S 171 GLN cc_start: 0.8837 (pm20) cc_final: 0.8564 (pm20) REVERT: S 180 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8991 (ptm) REVERT: S 189 ASP cc_start: 0.8894 (t0) cc_final: 0.8677 (p0) REVERT: S 210 GLU cc_start: 0.8184 (tp30) cc_final: 0.7132 (tp30) REVERT: S 222 GLU cc_start: 0.8755 (pm20) cc_final: 0.8321 (pm20) REVERT: S 234 GLU cc_start: 0.8234 (pm20) cc_final: 0.7927 (pm20) REVERT: A 65 MET cc_start: 0.7996 (tpt) cc_final: 0.7780 (tpt) REVERT: A 155 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6874 (p90) REVERT: A 180 MET cc_start: 0.7473 (tmm) cc_final: 0.6994 (tmm) outliers start: 52 outliers final: 39 residues processed: 195 average time/residue: 0.0910 time to fit residues: 24.7049 Evaluate side-chains 198 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 168 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.105831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076526 restraints weight = 18653.923| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.85 r_work: 0.3077 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8799 Z= 0.114 Angle : 0.579 6.767 11939 Z= 0.299 Chirality : 0.041 0.143 1352 Planarity : 0.004 0.051 1522 Dihedral : 4.136 41.751 1214 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.81 % Allowed : 28.67 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.26), residues: 1105 helix: 1.99 (0.28), residues: 353 sheet: 0.17 (0.33), residues: 271 loop : -0.92 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 168 TRP 0.014 0.001 TRP S 47 HIS 0.002 0.000 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8794) covalent geometry : angle 0.57871 (11929) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.63631 ( 10) hydrogen bonds : bond 0.03059 ( 399) hydrogen bonds : angle 4.26868 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: B 217 MET cc_start: 0.7685 (ppp) cc_final: 0.7394 (ppp) REVERT: B 254 ASP cc_start: 0.8854 (t70) cc_final: 0.8566 (t0) REVERT: B 262 MET cc_start: 0.9124 (mmm) cc_final: 0.8890 (mmm) REVERT: B 312 ASP cc_start: 0.9000 (t0) cc_final: 0.8614 (t0) REVERT: C 53 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4311 (ttt) REVERT: C 243 MET cc_start: 0.9332 (tpp) cc_final: 0.9117 (tpp) REVERT: C 298 GLU cc_start: 0.9127 (mp0) cc_final: 0.8907 (mp0) REVERT: C 331 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8009 (m-40) REVERT: C 346 ASN cc_start: 0.8955 (m110) cc_final: 0.8429 (m110) REVERT: G 21 MET cc_start: 0.9000 (mmp) cc_final: 0.8781 (mmp) REVERT: G 47 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8815 (mp0) REVERT: G 48 ASP cc_start: 0.8649 (t0) cc_final: 0.7658 (t0) REVERT: S 73 ASP cc_start: 0.8524 (t0) cc_final: 0.8190 (t0) REVERT: S 168 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8275 (mtt90) REVERT: S 171 GLN cc_start: 0.8794 (pm20) cc_final: 0.8550 (pm20) REVERT: S 180 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8971 (ptm) REVERT: S 210 GLU cc_start: 0.8261 (tp30) cc_final: 0.7363 (tp30) REVERT: S 211 ASP cc_start: 0.8086 (m-30) cc_final: 0.7710 (m-30) REVERT: S 222 GLU cc_start: 0.8750 (pm20) cc_final: 0.8329 (pm20) REVERT: S 234 GLU cc_start: 0.8235 (pm20) cc_final: 0.7920 (pm20) REVERT: A 155 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6861 (p90) REVERT: A 180 MET cc_start: 0.7436 (tmm) cc_final: 0.6967 (tmm) outliers start: 44 outliers final: 33 residues processed: 191 average time/residue: 0.0944 time to fit residues: 25.0829 Evaluate side-chains 195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 168 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.9990 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.104490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075002 restraints weight = 18875.872| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.87 r_work: 0.3053 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8799 Z= 0.144 Angle : 0.611 7.620 11939 Z= 0.315 Chirality : 0.042 0.151 1352 Planarity : 0.004 0.050 1522 Dihedral : 4.158 41.943 1213 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.81 % Allowed : 28.67 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1105 helix: 1.96 (0.28), residues: 353 sheet: 0.17 (0.33), residues: 265 loop : -0.94 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.010 0.001 PHE A 168 TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8794) covalent geometry : angle 0.61084 (11929) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.69601 ( 10) hydrogen bonds : bond 0.03261 ( 399) hydrogen bonds : angle 4.33577 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 59 TYR cc_start: 0.8731 (m-80) cc_final: 0.8356 (m-80) REVERT: B 217 MET cc_start: 0.7681 (ppp) cc_final: 0.7385 (ppp) REVERT: B 254 ASP cc_start: 0.8857 (t70) cc_final: 0.8544 (t0) REVERT: B 262 MET cc_start: 0.9116 (mmm) cc_final: 0.8875 (mmm) REVERT: B 312 ASP cc_start: 0.9011 (t0) cc_final: 0.8630 (t0) REVERT: C 53 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4416 (ttt) REVERT: C 243 MET cc_start: 0.9341 (tpp) cc_final: 0.9076 (tpp) REVERT: C 298 GLU cc_start: 0.9120 (mp0) cc_final: 0.8891 (mp0) REVERT: C 313 ARG cc_start: 0.8837 (mpt-90) cc_final: 0.8538 (mtt-85) REVERT: C 331 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: C 346 ASN cc_start: 0.8972 (m110) cc_final: 0.8703 (m110) REVERT: G 47 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8836 (mp0) REVERT: G 48 ASP cc_start: 0.8666 (t0) cc_final: 0.7770 (t0) REVERT: S 59 TYR cc_start: 0.8380 (m-10) cc_final: 0.8146 (m-10) REVERT: S 73 ASP cc_start: 0.8511 (t0) cc_final: 0.8173 (t0) REVERT: S 168 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8259 (mtt90) REVERT: S 171 GLN cc_start: 0.8799 (pm20) cc_final: 0.8525 (pm20) REVERT: S 180 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8991 (ptm) REVERT: S 210 GLU cc_start: 0.8220 (tp30) cc_final: 0.7333 (tp30) REVERT: S 222 GLU cc_start: 0.8753 (pm20) cc_final: 0.8311 (pm20) REVERT: S 234 GLU cc_start: 0.8195 (pm20) cc_final: 0.7900 (pm20) REVERT: A 65 MET cc_start: 0.7965 (tpt) cc_final: 0.7732 (tpt) REVERT: A 155 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6878 (p90) REVERT: A 180 MET cc_start: 0.7452 (tmm) cc_final: 0.7001 (tmm) outliers start: 44 outliers final: 34 residues processed: 186 average time/residue: 0.0941 time to fit residues: 24.1648 Evaluate side-chains 196 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 168 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 0.0050 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.105691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076163 restraints weight = 18703.945| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.86 r_work: 0.3074 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8799 Z= 0.123 Angle : 0.618 9.268 11939 Z= 0.316 Chirality : 0.042 0.152 1352 Planarity : 0.004 0.051 1522 Dihedral : 4.090 40.703 1213 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.49 % Allowed : 29.43 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1105 helix: 1.90 (0.28), residues: 359 sheet: 0.21 (0.33), residues: 271 loop : -0.96 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 168 TRP 0.014 0.001 TRP S 47 HIS 0.002 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8794) covalent geometry : angle 0.61763 (11929) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.60222 ( 10) hydrogen bonds : bond 0.03089 ( 399) hydrogen bonds : angle 4.28260 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: B 217 MET cc_start: 0.7686 (ppp) cc_final: 0.7387 (ppp) REVERT: B 254 ASP cc_start: 0.8840 (t70) cc_final: 0.8553 (t0) REVERT: B 262 MET cc_start: 0.9098 (mmm) cc_final: 0.8854 (mmm) REVERT: B 312 ASP cc_start: 0.8978 (t0) cc_final: 0.8596 (t0) REVERT: C 53 MET cc_start: 0.4933 (OUTLIER) cc_final: 0.4311 (ttt) REVERT: C 298 GLU cc_start: 0.9124 (mp0) cc_final: 0.8904 (mp0) REVERT: C 313 ARG cc_start: 0.8817 (mpt-90) cc_final: 0.8517 (mtt-85) REVERT: C 331 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (m-40) REVERT: C 346 ASN cc_start: 0.8965 (m110) cc_final: 0.8697 (m110) REVERT: G 17 GLU cc_start: 0.9252 (tp30) cc_final: 0.9046 (tp30) REVERT: G 20 LYS cc_start: 0.9377 (pttm) cc_final: 0.9154 (pptt) REVERT: G 47 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8814 (mp0) REVERT: G 48 ASP cc_start: 0.8672 (t0) cc_final: 0.7695 (t0) REVERT: S 73 ASP cc_start: 0.8547 (t0) cc_final: 0.8238 (t0) REVERT: S 168 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8365 (mtt90) REVERT: S 171 GLN cc_start: 0.8787 (pm20) cc_final: 0.8520 (pm20) REVERT: S 180 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8975 (ptm) REVERT: S 210 GLU cc_start: 0.8274 (tp30) cc_final: 0.7664 (tp30) REVERT: S 222 GLU cc_start: 0.8755 (pm20) cc_final: 0.8296 (pm20) REVERT: S 234 GLU cc_start: 0.8112 (pm20) cc_final: 0.7828 (pm20) REVERT: A 155 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6798 (p90) REVERT: A 180 MET cc_start: 0.7435 (tmm) cc_final: 0.6995 (tmm) REVERT: A 268 TYR cc_start: 0.8352 (m-80) cc_final: 0.7995 (m-80) outliers start: 41 outliers final: 35 residues processed: 186 average time/residue: 0.0982 time to fit residues: 25.2162 Evaluate side-chains 198 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 168 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.0870 chunk 106 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.106013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076254 restraints weight = 18662.363| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.89 r_work: 0.3081 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8799 Z= 0.121 Angle : 0.616 9.768 11939 Z= 0.312 Chirality : 0.042 0.149 1352 Planarity : 0.004 0.050 1522 Dihedral : 4.029 39.469 1213 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.70 % Allowed : 29.43 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.26), residues: 1105 helix: 1.88 (0.28), residues: 359 sheet: 0.22 (0.33), residues: 265 loop : -0.98 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 168 TRP 0.023 0.001 TRP S 47 HIS 0.002 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8794) covalent geometry : angle 0.61640 (11929) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.57826 ( 10) hydrogen bonds : bond 0.03091 ( 399) hydrogen bonds : angle 4.26887 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.12 seconds wall clock time: 39 minutes 27.28 seconds (2367.28 seconds total)