Starting phenix.real_space_refine on Mon May 12 15:00:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlq_36404/05_2025/8jlq_36404.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 67 5.16 5 Cl 1 4.86 5 C 5767 2.51 5 N 1541 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1902 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2294 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'G3C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.28, per 1000 atoms: 0.58 Number of scatterers: 9033 At special positions: 0 Unit cell: (107.12, 128.96, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 67 16.00 O 1657 8.00 N 1541 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 38.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.534A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.525A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.572A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.708A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.574A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.509A pdb=" N HIS R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 56 through 87 removed outlier: 4.269A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 124 Processing helix chain 'R' and resid 127 through 129 No H-bonds generated for 'chain 'R' and resid 127 through 129' Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 removed outlier: 4.201A pdb=" N ARG R 179 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 232 removed outlier: 3.871A pdb=" N ILE R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 277 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.966A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.330A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.809A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.911A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.554A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.446A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.240A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.744A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 5.457A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.910A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.910A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.143A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.899A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.44: 2616 1.44 - 1.57: 5074 1.57 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" CA HIS R 99 " pdb=" CB HIS R 99 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.57e-02 4.06e+03 2.79e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.234 1.170 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta sigma weight residual 1.457 1.393 0.064 1.29e-02 6.01e+03 2.48e+01 bond pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.16e-02 7.43e+03 2.39e+01 bond pdb=" CA PHE R 154 " pdb=" C PHE R 154 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.28e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 12243 2.44 - 4.88: 228 4.88 - 7.31: 29 7.31 - 9.75: 4 9.75 - 12.19: 1 Bond angle restraints: 12505 Sorted by residual: angle pdb=" C ARG A 283 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 122.21 110.02 12.19 1.48e+00 4.57e-01 6.78e+01 angle pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta sigma weight residual 122.89 115.22 7.67 1.12e+00 7.97e-01 4.69e+01 angle pdb=" N VAL R 184 " pdb=" CA VAL R 184 " pdb=" C VAL R 184 " ideal model delta sigma weight residual 109.37 116.64 -7.27 1.35e+00 5.49e-01 2.90e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" CB TYR A 358 " ideal model delta sigma weight residual 111.43 103.57 7.86 1.59e+00 3.96e-01 2.44e+01 angle pdb=" N THR B 223 " pdb=" CA THR B 223 " pdb=" C THR B 223 " ideal model delta sigma weight residual 110.17 102.80 7.37 1.51e+00 4.39e-01 2.38e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4954 16.77 - 33.53: 412 33.53 - 50.30: 101 50.30 - 67.07: 9 67.07 - 83.84: 6 Dihedral angle restraints: 5482 sinusoidal: 2165 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -148.00 62.00 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C ARG B 134 " pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" CB ARG B 134 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 265 0.108 - 0.162: 35 0.162 - 0.216: 7 0.216 - 0.270: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG B 134 " pdb=" N ARG B 134 " pdb=" C ARG B 134 " pdb=" CB ARG B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 220 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN R 220 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN R 220 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA R 221 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 99 " -0.028 2.00e-02 2.50e+03 2.33e-02 8.16e+00 pdb=" CG HIS R 99 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS R 99 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS R 99 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS R 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 292 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C PHE R 292 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE R 292 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY R 293 " 0.016 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 827 2.74 - 3.28: 9477 3.28 - 3.82: 16137 3.82 - 4.36: 19073 4.36 - 4.90: 32353 Nonbonded interactions: 77867 Sorted by model distance: nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR S 175 " model vdw 2.203 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.210 3.040 nonbonded pdb=" ND1 HIS A 387 " pdb=" O ALA R 124 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.261 3.040 ... (remaining 77862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 : 0.005 0.083 9241 Z= 0.328 Angle : 0.783 12.189 12513 Z= 0.475 Chirality : 0.047 0.270 1393 Planarity : 0.005 0.044 1577 Dihedral : 13.144 83.836 3330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.41 % Allowed : 1.02 % Favored : 98.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1120 helix: 0.90 (0.26), residues: 403 sheet: -0.51 (0.32), residues: 270 loop : -1.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.016 0.001 HIS R 99 PHE 0.018 0.001 PHE R 154 TYR 0.029 0.002 TYR A 358 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.15097 ( 458) hydrogen bonds : angle 7.02175 ( 1326) SS BOND : bond 0.00727 ( 4) SS BOND : angle 1.62150 ( 8) covalent geometry : bond 0.00481 ( 9237) covalent geometry : angle 0.78206 (12505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 65 MET cc_start: 0.7214 (ttp) cc_final: 0.7003 (mtp) REVERT: Y 32 LYS cc_start: 0.8155 (tttm) cc_final: 0.7781 (tppt) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 1.0303 time to fit residues: 192.3718 Evaluate side-chains 140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.0050 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 156 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.245565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191273 restraints weight = 10121.025| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.41 r_work: 0.3964 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9241 Z= 0.134 Angle : 0.611 6.806 12513 Z= 0.322 Chirality : 0.044 0.195 1393 Planarity : 0.005 0.044 1577 Dihedral : 4.737 51.223 1261 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.04 % Allowed : 10.08 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1120 helix: 1.47 (0.25), residues: 397 sheet: -0.38 (0.33), residues: 265 loop : -1.10 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.004 0.001 HIS R 55 PHE 0.017 0.001 PHE R 299 TYR 0.015 0.001 TYR A 37 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 458) hydrogen bonds : angle 5.59738 ( 1326) SS BOND : bond 0.00848 ( 4) SS BOND : angle 1.34639 ( 8) covalent geometry : bond 0.00292 ( 9237) covalent geometry : angle 0.61071 (12505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7260 (mtp180) cc_final: 0.6538 (pmm150) REVERT: B 134 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.7224 (ptt-90) REVERT: B 249 THR cc_start: 0.7680 (p) cc_final: 0.7465 (p) REVERT: R 59 ASN cc_start: 0.7920 (m-40) cc_final: 0.7649 (m-40) REVERT: R 65 MET cc_start: 0.7594 (ttp) cc_final: 0.7270 (ttp) REVERT: R 220 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: S 38 ARG cc_start: 0.5605 (ptt180) cc_final: 0.5236 (ptt180) REVERT: S 192 MET cc_start: 0.2928 (pp-130) cc_final: 0.2479 (ppp) REVERT: Y 32 LYS cc_start: 0.8331 (tttm) cc_final: 0.7533 (tppt) outliers start: 20 outliers final: 5 residues processed: 156 average time/residue: 0.9927 time to fit residues: 167.1156 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 220 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 0.0970 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 183 HIS B 220 GLN B 268 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.243860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.188166 restraints weight = 10192.474| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.59 r_work: 0.3921 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9241 Z= 0.128 Angle : 0.584 8.593 12513 Z= 0.305 Chirality : 0.043 0.180 1393 Planarity : 0.004 0.046 1577 Dihedral : 4.260 22.792 1256 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.75 % Allowed : 12.63 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1120 helix: 1.58 (0.25), residues: 398 sheet: -0.28 (0.33), residues: 267 loop : -1.13 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.014 0.001 TYR A 37 ARG 0.005 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 458) hydrogen bonds : angle 5.35056 ( 1326) SS BOND : bond 0.00604 ( 4) SS BOND : angle 1.33123 ( 8) covalent geometry : bond 0.00278 ( 9237) covalent geometry : angle 0.58273 (12505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6409 (pmm150) REVERT: B 132 ASN cc_start: 0.6762 (m-40) cc_final: 0.6205 (p0) REVERT: B 197 ARG cc_start: 0.6544 (mmm-85) cc_final: 0.6232 (mmp80) REVERT: R 59 ASN cc_start: 0.7921 (m-40) cc_final: 0.7673 (m-40) REVERT: R 65 MET cc_start: 0.7734 (ttp) cc_final: 0.7519 (ttp) REVERT: R 158 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.6165 (ttm) REVERT: R 220 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: S 38 ARG cc_start: 0.5461 (ptt180) cc_final: 0.5176 (ptt180) REVERT: Y 32 LYS cc_start: 0.8304 (tttm) cc_final: 0.7501 (tppt) outliers start: 27 outliers final: 6 residues processed: 145 average time/residue: 0.9959 time to fit residues: 156.6906 Evaluate side-chains 135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.237595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.175103 restraints weight = 10012.899| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.25 r_work: 0.3857 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9241 Z= 0.185 Angle : 0.639 8.479 12513 Z= 0.332 Chirality : 0.045 0.168 1393 Planarity : 0.004 0.044 1577 Dihedral : 4.437 24.686 1256 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.36 % Allowed : 14.56 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1120 helix: 1.58 (0.25), residues: 398 sheet: -0.17 (0.33), residues: 269 loop : -1.05 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 148 HIS 0.006 0.002 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.015 0.002 TYR A 37 ARG 0.005 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 458) hydrogen bonds : angle 5.37798 ( 1326) SS BOND : bond 0.00992 ( 4) SS BOND : angle 1.93152 ( 8) covalent geometry : bond 0.00423 ( 9237) covalent geometry : angle 0.63707 (12505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ASN cc_start: 0.6803 (m-40) cc_final: 0.6268 (p0) REVERT: B 134 ARG cc_start: 0.7844 (ptp-170) cc_final: 0.7587 (ptp-170) REVERT: B 336 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (tt) REVERT: R 31 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7385 (m) REVERT: R 65 MET cc_start: 0.8019 (ttp) cc_final: 0.7798 (ttp) REVERT: R 123 TYR cc_start: 0.8413 (m-80) cc_final: 0.8121 (m-80) REVERT: R 158 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6484 (ttm) REVERT: S 38 ARG cc_start: 0.5426 (ptt180) cc_final: 0.5096 (ptt180) REVERT: S 93 MET cc_start: 0.6624 (mmm) cc_final: 0.6411 (mmm) REVERT: Y 32 LYS cc_start: 0.8279 (tttm) cc_final: 0.7505 (tppt) outliers start: 33 outliers final: 13 residues processed: 151 average time/residue: 0.9844 time to fit residues: 160.6992 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 96 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 32 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 99 HIS R 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.240184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182786 restraints weight = 10076.478| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.55 r_work: 0.3878 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9241 Z= 0.135 Angle : 0.615 12.137 12513 Z= 0.314 Chirality : 0.044 0.400 1393 Planarity : 0.004 0.052 1577 Dihedral : 4.300 24.826 1256 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 17.01 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1120 helix: 1.64 (0.25), residues: 398 sheet: -0.17 (0.33), residues: 266 loop : -1.05 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS R 55 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR R 200 ARG 0.007 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 458) hydrogen bonds : angle 5.23028 ( 1326) SS BOND : bond 0.00694 ( 4) SS BOND : angle 1.31519 ( 8) covalent geometry : bond 0.00305 ( 9237) covalent geometry : angle 0.61396 (12505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7785 (ptp-170) cc_final: 0.7418 (ptt-90) REVERT: B 219 ARG cc_start: 0.7424 (mmp80) cc_final: 0.7065 (mmp80) REVERT: R 31 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7533 (m) REVERT: R 65 MET cc_start: 0.7684 (ttp) cc_final: 0.7458 (ttp) REVERT: R 158 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6490 (ttm) REVERT: R 220 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: S 34 MET cc_start: 0.6844 (mmp) cc_final: 0.6623 (mmp) REVERT: S 38 ARG cc_start: 0.5390 (ptt180) cc_final: 0.5159 (ptt180) REVERT: S 140 MET cc_start: 0.5454 (mmm) cc_final: 0.4306 (ttp) REVERT: Y 32 LYS cc_start: 0.8323 (tttm) cc_final: 0.7590 (tppt) outliers start: 28 outliers final: 12 residues processed: 150 average time/residue: 1.0490 time to fit residues: 169.6268 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.238741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.177248 restraints weight = 10073.479| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.50 r_work: 0.3861 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9241 Z= 0.151 Angle : 0.636 10.816 12513 Z= 0.321 Chirality : 0.044 0.265 1393 Planarity : 0.004 0.051 1577 Dihedral : 4.355 25.042 1256 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.95 % Allowed : 17.62 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1120 helix: 1.66 (0.25), residues: 397 sheet: -0.17 (0.33), residues: 266 loop : -1.05 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 60 HIS 0.004 0.001 HIS R 55 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.002 TYR A 37 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 458) hydrogen bonds : angle 5.21297 ( 1326) SS BOND : bond 0.00830 ( 4) SS BOND : angle 1.51764 ( 8) covalent geometry : bond 0.00348 ( 9237) covalent geometry : angle 0.63525 (12505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6174 (pm20) cc_final: 0.5766 (mm-30) REVERT: B 134 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7379 (ptt-90) REVERT: B 219 ARG cc_start: 0.7449 (mmp80) cc_final: 0.7072 (mmp80) REVERT: R 31 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7518 (m) REVERT: R 65 MET cc_start: 0.7754 (ttp) cc_final: 0.7494 (ttp) REVERT: R 158 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6571 (ttm) REVERT: R 220 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: S 38 ARG cc_start: 0.5330 (ptt180) cc_final: 0.5103 (ptt180) REVERT: Y 32 LYS cc_start: 0.8354 (tttm) cc_final: 0.7585 (tppt) outliers start: 29 outliers final: 13 residues processed: 143 average time/residue: 1.0303 time to fit residues: 159.6430 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 30.0000 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.238803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181441 restraints weight = 10235.152| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.53 r_work: 0.3863 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9241 Z= 0.146 Angle : 0.640 9.566 12513 Z= 0.323 Chirality : 0.044 0.198 1393 Planarity : 0.004 0.054 1577 Dihedral : 4.342 25.188 1256 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.55 % Allowed : 19.04 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1120 helix: 1.61 (0.25), residues: 397 sheet: -0.15 (0.33), residues: 264 loop : -1.09 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 60 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.002 TYR A 37 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 458) hydrogen bonds : angle 5.19020 ( 1326) SS BOND : bond 0.00736 ( 4) SS BOND : angle 1.39801 ( 8) covalent geometry : bond 0.00337 ( 9237) covalent geometry : angle 0.63891 (12505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.5957 (pm20) cc_final: 0.5722 (mm-30) REVERT: B 134 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7384 (ptt-90) REVERT: B 219 ARG cc_start: 0.7415 (mmp80) cc_final: 0.6987 (mmp80) REVERT: B 262 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7280 (ttm) REVERT: R 31 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7328 (m) REVERT: R 65 MET cc_start: 0.7693 (ttp) cc_final: 0.7490 (ttp) REVERT: R 123 TYR cc_start: 0.8281 (m-80) cc_final: 0.8061 (m-80) REVERT: R 158 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6589 (ttm) REVERT: R 220 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: S 38 ARG cc_start: 0.5322 (ptt180) cc_final: 0.5085 (ptt180) REVERT: S 93 MET cc_start: 0.6692 (mmm) cc_final: 0.6080 (mmm) REVERT: Y 32 LYS cc_start: 0.8360 (tttm) cc_final: 0.7593 (tppt) outliers start: 25 outliers final: 12 residues processed: 142 average time/residue: 1.1553 time to fit residues: 175.8563 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.238290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181239 restraints weight = 10379.899| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.51 r_work: 0.3859 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9241 Z= 0.148 Angle : 0.643 11.436 12513 Z= 0.325 Chirality : 0.045 0.269 1393 Planarity : 0.004 0.053 1577 Dihedral : 4.349 25.253 1256 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.44 % Allowed : 18.94 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1120 helix: 1.58 (0.25), residues: 398 sheet: -0.20 (0.33), residues: 255 loop : -1.08 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 60 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.001 TYR S 190 ARG 0.009 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 458) hydrogen bonds : angle 5.14918 ( 1326) SS BOND : bond 0.00720 ( 4) SS BOND : angle 1.66986 ( 8) covalent geometry : bond 0.00340 ( 9237) covalent geometry : angle 0.64198 (12505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8577 (ttp) cc_final: 0.8296 (ttm) REVERT: B 134 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7528 (ptt-90) REVERT: B 180 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.4383 (p90) REVERT: B 219 ARG cc_start: 0.7399 (mmp80) cc_final: 0.6981 (mmp80) REVERT: B 275 SER cc_start: 0.8390 (t) cc_final: 0.8090 (p) REVERT: R 31 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7453 (m) REVERT: R 123 TYR cc_start: 0.8300 (m-80) cc_final: 0.7958 (m-80) REVERT: R 158 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6611 (ttm) REVERT: R 220 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: Y 32 LYS cc_start: 0.8367 (tttm) cc_final: 0.7587 (tppt) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 1.1074 time to fit residues: 167.6418 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.238117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181034 restraints weight = 10179.121| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.56 r_work: 0.3841 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9241 Z= 0.154 Angle : 0.648 9.854 12513 Z= 0.328 Chirality : 0.045 0.220 1393 Planarity : 0.005 0.061 1577 Dihedral : 4.400 25.516 1256 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.34 % Allowed : 20.16 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1120 helix: 1.61 (0.25), residues: 398 sheet: -0.16 (0.32), residues: 265 loop : -1.03 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 60 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.002 TYR S 190 ARG 0.008 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 458) hydrogen bonds : angle 5.18159 ( 1326) SS BOND : bond 0.00786 ( 4) SS BOND : angle 1.76443 ( 8) covalent geometry : bond 0.00356 ( 9237) covalent geometry : angle 0.64700 (12505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8092 (m-30) cc_final: 0.7859 (m-30) REVERT: B 55 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 134 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7436 (ptt-90) REVERT: B 180 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.4329 (p90) REVERT: B 219 ARG cc_start: 0.7400 (mmp80) cc_final: 0.7002 (mmp80) REVERT: B 262 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7280 (ttm) REVERT: R 31 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7439 (m) REVERT: R 65 MET cc_start: 0.7532 (ttp) cc_final: 0.7068 (mtp) REVERT: R 123 TYR cc_start: 0.8309 (m-80) cc_final: 0.7923 (m-80) REVERT: R 158 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6619 (ttm) REVERT: R 220 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: S 38 ARG cc_start: 0.5362 (ptt180) cc_final: 0.5061 (ptt180) REVERT: Y 32 LYS cc_start: 0.8325 (tttm) cc_final: 0.7573 (tppt) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 1.1196 time to fit residues: 161.4061 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.237234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179661 restraints weight = 10220.366| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.52 r_work: 0.3832 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9241 Z= 0.168 Angle : 0.673 10.322 12513 Z= 0.340 Chirality : 0.045 0.195 1393 Planarity : 0.005 0.060 1577 Dihedral : 4.440 25.625 1256 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.44 % Allowed : 20.47 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1120 helix: 1.58 (0.25), residues: 398 sheet: -0.19 (0.33), residues: 265 loop : -1.01 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 60 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE R 299 TYR 0.015 0.002 TYR S 190 ARG 0.009 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 458) hydrogen bonds : angle 5.21278 ( 1326) SS BOND : bond 0.00704 ( 4) SS BOND : angle 2.14793 ( 8) covalent geometry : bond 0.00389 ( 9237) covalent geometry : angle 0.67141 (12505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8125 (m-30) cc_final: 0.7794 (m-30) REVERT: B 55 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 180 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.4445 (p90) REVERT: B 219 ARG cc_start: 0.7401 (mmp80) cc_final: 0.6998 (mmp80) REVERT: B 262 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7247 (ttm) REVERT: R 31 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7397 (m) REVERT: R 65 MET cc_start: 0.7640 (ttp) cc_final: 0.7296 (ttp) REVERT: R 123 TYR cc_start: 0.8299 (m-80) cc_final: 0.7913 (m-80) REVERT: R 158 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6624 (ttm) REVERT: R 220 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: S 93 MET cc_start: 0.6679 (mmm) cc_final: 0.5882 (mmm) REVERT: Y 32 LYS cc_start: 0.8312 (tttm) cc_final: 0.7563 (tppt) outliers start: 24 outliers final: 12 residues processed: 134 average time/residue: 1.0980 time to fit residues: 158.5153 Evaluate side-chains 135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 89 optimal weight: 0.0170 chunk 101 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.237047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.178912 restraints weight = 10148.570| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.46 r_work: 0.3847 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 9241 Z= 0.264 Angle : 0.982 59.194 12513 Z= 0.572 Chirality : 0.047 0.491 1393 Planarity : 0.005 0.057 1577 Dihedral : 4.508 28.333 1256 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.34 % Allowed : 21.18 % Favored : 76.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1120 helix: 1.59 (0.25), residues: 398 sheet: -0.19 (0.33), residues: 265 loop : -0.99 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 60 HIS 0.004 0.001 HIS A 220 PHE 0.019 0.001 PHE R 299 TYR 0.014 0.002 TYR R 200 ARG 0.018 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 458) hydrogen bonds : angle 5.22571 ( 1326) SS BOND : bond 0.00850 ( 4) SS BOND : angle 2.07285 ( 8) covalent geometry : bond 0.00536 ( 9237) covalent geometry : angle 0.98044 (12505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6989.79 seconds wall clock time: 121 minutes 18.05 seconds (7278.05 seconds total)