Starting phenix.real_space_refine on Sun Apr 5 06:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.map" model { file = "/net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9llh_63202/04_2026/9llh_63202.cif" } resolution = 2.73 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= 0.076 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 54 5.16 5 C 5572 2.51 5 N 1507 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8706 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1819 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "M" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 640 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2221 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.23 Number of scatterers: 8706 At special positions: 0 Unit cell: (78.12, 103.23, 131.13, 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 54 16.00 O 1573 8.00 N 1507 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 0.72 Conformation dependent library (CDL) restraints added in 249.2 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.739A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.009A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.918A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.879A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.977A pdb=" N SER C 8 " --> pdb=" O ASN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.157A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.506A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'M' and resid 9 through 39 Processing helix chain 'M' and resid 46 through 75 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.624A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 22 through 51 Processing helix chain 'R' and resid 51 through 57 removed outlier: 3.681A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 4.298A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 94 through 127 removed outlier: 3.957A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN R 113 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER R 127 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 154 Processing helix chain 'R' and resid 155 through 161 Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 241 Processing helix chain 'R' and resid 263 through 295 removed outlier: 4.456A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.824A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 309 through 323 Processing helix chain 'R' and resid 326 through 332 Processing helix chain 'R' and resid 334 through 344 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.682A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.324A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.419A 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: 6.962A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.532A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.981A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.727A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.147A 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: 3.532A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.084A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1356 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: 1.15 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2797 1.34 - 1.46: 1938 1.46 - 1.58: 4081 1.58 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8889 Sorted by residual: bond pdb=" C4 LDP R 701 " pdb=" O2 LDP R 701 " ideal model delta sigma weight residual 1.355 1.401 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C3 LDP R 701 " pdb=" O1 LDP R 701 " ideal model delta sigma weight residual 1.353 1.398 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 LDP R 701 " pdb=" C7 LDP R 701 " ideal model delta sigma weight residual 1.502 1.525 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" CA ILE R 205 " pdb=" CB ILE R 205 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 1.01e+00 bond pdb=" N PRO R 91 " pdb=" CA PRO R 91 " ideal model delta sigma weight residual 1.473 1.466 0.007 8.50e-03 1.38e+04 6.97e-01 ... (remaining 8884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 11754 1.29 - 2.58: 223 2.58 - 3.86: 45 3.86 - 5.15: 16 5.15 - 6.44: 2 Bond angle restraints: 12040 Sorted by residual: angle pdb=" N ILE R 98 " pdb=" CA ILE R 98 " pdb=" C ILE R 98 " ideal model delta sigma weight residual 113.39 108.68 4.71 1.47e+00 4.63e-01 1.03e+01 angle pdb=" OG1 THR A 285 " pdb=" CB THR A 285 " pdb=" CG2 THR A 285 " ideal model delta sigma weight residual 109.30 103.28 6.02 2.00e+00 2.50e-01 9.06e+00 angle pdb=" C HIS A 362 " pdb=" N PHE A 363 " pdb=" CA PHE A 363 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.34e+00 angle pdb=" C CYS B 250 " pdb=" N ARG B 251 " pdb=" CA ARG B 251 " ideal model delta sigma weight residual 121.80 117.99 3.81 1.71e+00 3.42e-01 4.96e+00 angle pdb=" CA ILE R 98 " pdb=" C ILE R 98 " pdb=" N TRP R 99 " ideal model delta sigma weight residual 118.55 116.65 1.90 8.60e-01 1.35e+00 4.87e+00 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5099 17.83 - 35.66: 170 35.66 - 53.49: 22 53.49 - 71.32: 3 71.32 - 89.15: 4 Dihedral angle restraints: 5298 sinusoidal: 2097 harmonic: 3201 Sorted by residual: dihedral pdb=" CA THR N 114 " pdb=" C THR N 114 " pdb=" N TYR N 115 " pdb=" CA TYR N 115 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR N 115 " pdb=" C TYR N 115 " pdb=" N ALA N 116 " pdb=" CA ALA N 116 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 916 0.034 - 0.068: 322 0.068 - 0.101: 92 0.101 - 0.135: 38 0.135 - 0.169: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CB THR A 285 " pdb=" CA THR A 285 " pdb=" OG1 THR A 285 " pdb=" CG2 THR A 285 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VAL A 248 " pdb=" N VAL A 248 " pdb=" C VAL A 248 " pdb=" CB VAL A 248 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1367 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 117 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ILE R 117 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 117 " -0.011 2.00e-02 2.50e+03 pdb=" N SER R 118 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 120 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ASP R 120 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP R 120 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG R 121 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 236 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 662 2.74 - 3.28: 8704 3.28 - 3.82: 14779 3.82 - 4.36: 17820 4.36 - 4.90: 30664 Nonbonded interactions: 72629 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.260 3.040 nonbonded pdb=" OG SER R 198 " pdb=" O2 LDP R 701 " model vdw 2.279 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.280 3.120 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.293 3.040 ... (remaining 72624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8893 Z= 0.137 Angle : 0.493 6.438 12048 Z= 0.276 Chirality : 0.040 0.169 1370 Planarity : 0.004 0.041 1512 Dihedral : 9.504 89.147 3200 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1069 helix: 1.95 (0.24), residues: 442 sheet: 0.54 (0.34), residues: 207 loop : -0.08 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR A 37 PHE 0.014 0.001 PHE B 199 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8889) covalent geometry : angle 0.49267 (12040) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.87177 ( 8) hydrogen bonds : bond 0.14227 ( 481) hydrogen bonds : angle 6.24065 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 386 MET cc_start: 0.7877 (ttp) cc_final: 0.7661 (ttm) REVERT: B 96 ARG cc_start: 0.7381 (mtp180) cc_final: 0.6763 (mtp-110) REVERT: B 101 MET cc_start: 0.8252 (mtp) cc_final: 0.7843 (mtp) REVERT: B 252 LEU cc_start: 0.6053 (tt) cc_final: 0.5553 (tp) REVERT: C 44 HIS cc_start: 0.7081 (m-70) cc_final: 0.6270 (t-170) REVERT: N 52 SER cc_start: 0.6714 (p) cc_final: 0.6512 (m) outliers start: 0 outliers final: 1 residues processed: 218 average time/residue: 0.6113 time to fit residues: 140.7109 Evaluate side-chains 139 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 292 ASN R 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.202828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168632 restraints weight = 10304.774| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.98 r_work: 0.3881 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8893 Z= 0.126 Angle : 0.528 8.371 12048 Z= 0.282 Chirality : 0.041 0.248 1370 Planarity : 0.004 0.042 1512 Dihedral : 4.382 25.392 1190 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.22 % Allowed : 10.13 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1069 helix: 2.49 (0.23), residues: 451 sheet: 0.61 (0.33), residues: 210 loop : -0.06 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.018 0.001 TYR M 34 PHE 0.021 0.002 PHE M 53 TRP 0.014 0.001 TRP M 18 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8889) covalent geometry : angle 0.52780 (12040) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.62617 ( 8) hydrogen bonds : bond 0.05084 ( 481) hydrogen bonds : angle 4.47963 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.6562 (mp0) cc_final: 0.6336 (tm-30) REVERT: A 380 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7658 (ttt90) REVERT: B 59 TYR cc_start: 0.7949 (m-80) cc_final: 0.7688 (m-80) REVERT: B 96 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7104 (mtp-110) REVERT: B 101 MET cc_start: 0.8445 (mtp) cc_final: 0.7987 (mtp) REVERT: B 217 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7471 (pmt) REVERT: B 252 LEU cc_start: 0.6115 (tt) cc_final: 0.5611 (tp) REVERT: C 44 HIS cc_start: 0.6553 (m-70) cc_final: 0.6029 (t-170) REVERT: N 46 GLU cc_start: 0.7557 (pt0) cc_final: 0.7182 (mt-10) REVERT: R 197 SER cc_start: 0.7199 (t) cc_final: 0.6635 (p) outliers start: 21 outliers final: 9 residues processed: 158 average time/residue: 0.5396 time to fit residues: 91.0071 Evaluate side-chains 140 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 156 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4316 r_free = 0.4316 target = 0.199793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165722 restraints weight = 10312.186| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.96 r_work: 0.3838 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8893 Z= 0.141 Angle : 0.538 7.435 12048 Z= 0.285 Chirality : 0.042 0.193 1370 Planarity : 0.004 0.044 1512 Dihedral : 4.414 23.199 1188 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.06 % Allowed : 10.65 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1069 helix: 2.37 (0.23), residues: 451 sheet: 0.51 (0.34), residues: 210 loop : -0.20 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 38 TYR 0.013 0.002 TYR M 34 PHE 0.017 0.002 PHE N 108 TRP 0.014 0.002 TRP M 18 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8889) covalent geometry : angle 0.53759 (12040) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.71261 ( 8) hydrogen bonds : bond 0.04934 ( 481) hydrogen bonds : angle 4.38417 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7404 (mtm180) cc_final: 0.6795 (mtt-85) REVERT: A 289 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8168 (tt) REVERT: A 293 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6808 (mmtt) REVERT: B 96 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7125 (mtp-110) REVERT: B 101 MET cc_start: 0.8478 (mtp) cc_final: 0.8101 (mtp) REVERT: B 217 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7482 (pmt) REVERT: B 252 LEU cc_start: 0.6096 (tt) cc_final: 0.5660 (tp) REVERT: M 69 LEU cc_start: 0.8163 (mp) cc_final: 0.7904 (mp) REVERT: N 46 GLU cc_start: 0.7501 (pt0) cc_final: 0.6886 (mt-10) REVERT: R 134 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (mttp) REVERT: R 292 ASN cc_start: 0.7913 (t0) cc_final: 0.7627 (t0) outliers start: 29 outliers final: 10 residues processed: 161 average time/residue: 0.5493 time to fit residues: 94.3405 Evaluate side-chains 142 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 134 LYS Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 4 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4337 r_free = 0.4337 target = 0.202560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.168575 restraints weight = 10523.742| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.98 r_work: 0.3868 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8893 Z= 0.110 Angle : 0.503 8.349 12048 Z= 0.265 Chirality : 0.040 0.206 1370 Planarity : 0.004 0.041 1512 Dihedral : 4.186 25.585 1188 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.53 % Allowed : 13.08 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.25), residues: 1069 helix: 2.42 (0.23), residues: 451 sheet: 0.72 (0.35), residues: 198 loop : -0.18 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.013 0.001 TYR N 60 PHE 0.017 0.001 PHE N 27 TRP 0.013 0.001 TRP M 18 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8889) covalent geometry : angle 0.50268 (12040) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.49806 ( 8) hydrogen bonds : bond 0.04382 ( 481) hydrogen bonds : angle 4.21893 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.355 Fit side-chains REVERT: A 283 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6811 (mtt-85) REVERT: B 46 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7425 (mpp-170) REVERT: B 59 TYR cc_start: 0.7973 (m-80) cc_final: 0.7709 (m-80) REVERT: B 96 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7097 (mtp-110) REVERT: B 101 MET cc_start: 0.8383 (mtp) cc_final: 0.8014 (mtp) REVERT: B 217 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7551 (pmt) REVERT: B 252 LEU cc_start: 0.6012 (tt) cc_final: 0.5616 (tp) REVERT: M 69 LEU cc_start: 0.8168 (mp) cc_final: 0.7906 (mp) REVERT: R 134 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7971 (mttp) REVERT: R 213 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7539 (p) REVERT: R 271 LEU cc_start: 0.8095 (mt) cc_final: 0.7804 (tp) REVERT: R 292 ASN cc_start: 0.7741 (t0) cc_final: 0.7055 (t0) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 0.5599 time to fit residues: 93.0052 Evaluate side-chains 145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 134 LYS Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 40.0000 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4259 r_free = 0.4259 target = 0.193633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160413 restraints weight = 10487.236| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.87 r_work: 0.3767 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 8893 Z= 0.232 Angle : 0.630 8.687 12048 Z= 0.334 Chirality : 0.045 0.193 1370 Planarity : 0.005 0.066 1512 Dihedral : 4.874 26.825 1188 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.01 % Allowed : 12.45 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1069 helix: 1.90 (0.23), residues: 455 sheet: 0.35 (0.34), residues: 206 loop : -0.74 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 256 TYR 0.017 0.002 TYR A 339 PHE 0.025 0.002 PHE N 108 TRP 0.018 0.003 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8889) covalent geometry : angle 0.63001 (12040) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.89650 ( 8) hydrogen bonds : bond 0.05542 ( 481) hydrogen bonds : angle 4.56395 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 293 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6615 (mmtt) REVERT: B 101 MET cc_start: 0.8481 (mtp) cc_final: 0.8095 (mtp) REVERT: B 205 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8162 (p0) REVERT: B 252 LEU cc_start: 0.6248 (tt) cc_final: 0.5810 (tp) REVERT: B 304 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6461 (ttm170) REVERT: M 69 LEU cc_start: 0.8244 (mp) cc_final: 0.7982 (mp) outliers start: 38 outliers final: 20 residues processed: 169 average time/residue: 0.5192 time to fit residues: 93.8827 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.0020 chunk 87 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.198035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163651 restraints weight = 10371.098| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.96 r_work: 0.3826 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8893 Z= 0.126 Angle : 0.546 8.912 12048 Z= 0.285 Chirality : 0.041 0.186 1370 Planarity : 0.004 0.042 1512 Dihedral : 4.497 25.413 1188 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.06 % Allowed : 14.14 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1069 helix: 2.19 (0.23), residues: 455 sheet: 0.36 (0.34), residues: 206 loop : -0.66 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 38 TYR 0.017 0.002 TYR M 34 PHE 0.028 0.002 PHE M 53 TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8889) covalent geometry : angle 0.54567 (12040) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.53062 ( 8) hydrogen bonds : bond 0.04615 ( 481) hydrogen bonds : angle 4.33375 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.343 Fit side-chains REVERT: A 283 ARG cc_start: 0.7438 (mtm110) cc_final: 0.6686 (mtt-85) REVERT: A 380 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7654 (ttt-90) REVERT: B 46 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7296 (mpp-170) REVERT: B 101 MET cc_start: 0.8471 (mtp) cc_final: 0.8068 (mtp) REVERT: B 252 LEU cc_start: 0.6156 (tt) cc_final: 0.5718 (tp) REVERT: M 51 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6955 (tpp80) REVERT: M 69 LEU cc_start: 0.8175 (mp) cc_final: 0.7894 (mp) REVERT: R 98 ILE cc_start: 0.7066 (tp) cc_final: 0.6813 (mm) REVERT: R 292 ASN cc_start: 0.7865 (t0) cc_final: 0.7593 (t0) outliers start: 29 outliers final: 17 residues processed: 153 average time/residue: 0.5348 time to fit residues: 87.4006 Evaluate side-chains 145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4296 r_free = 0.4296 target = 0.197799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165097 restraints weight = 10390.649| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.90 r_work: 0.3823 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8893 Z= 0.131 Angle : 0.538 9.082 12048 Z= 0.283 Chirality : 0.041 0.211 1370 Planarity : 0.004 0.050 1512 Dihedral : 4.402 27.028 1188 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.38 % Allowed : 15.08 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1069 helix: 2.23 (0.23), residues: 455 sheet: 0.46 (0.35), residues: 198 loop : -0.71 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 38 TYR 0.013 0.001 TYR A 37 PHE 0.018 0.002 PHE N 27 TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8889) covalent geometry : angle 0.53814 (12040) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.53469 ( 8) hydrogen bonds : bond 0.04538 ( 481) hydrogen bonds : angle 4.29353 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.239 Fit side-chains REVERT: A 283 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6652 (mtt-85) REVERT: A 347 ARG cc_start: 0.7682 (ptm160) cc_final: 0.7198 (ttp-110) REVERT: B 46 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7270 (mpp-170) REVERT: B 101 MET cc_start: 0.8508 (mtp) cc_final: 0.8108 (mtp) REVERT: B 217 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7548 (pmt) REVERT: B 252 LEU cc_start: 0.6038 (tt) cc_final: 0.5624 (tp) REVERT: M 69 LEU cc_start: 0.8189 (mp) cc_final: 0.7907 (mp) REVERT: R 98 ILE cc_start: 0.7051 (tp) cc_final: 0.6817 (mm) outliers start: 32 outliers final: 19 residues processed: 151 average time/residue: 0.5028 time to fit residues: 81.3457 Evaluate side-chains 145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 4 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4297 r_free = 0.4297 target = 0.197802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163272 restraints weight = 10371.198| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.99 r_work: 0.3817 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8893 Z= 0.135 Angle : 0.563 11.730 12048 Z= 0.293 Chirality : 0.041 0.216 1370 Planarity : 0.004 0.044 1512 Dihedral : 4.412 26.855 1188 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.85 % Allowed : 15.82 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1069 helix: 2.32 (0.23), residues: 449 sheet: 0.61 (0.36), residues: 191 loop : -0.76 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.013 0.002 TYR A 339 PHE 0.031 0.002 PHE M 53 TRP 0.016 0.002 TRP A 234 HIS 0.014 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8889) covalent geometry : angle 0.56291 (12040) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.55484 ( 8) hydrogen bonds : bond 0.04511 ( 481) hydrogen bonds : angle 4.29080 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7475 (mtm110) cc_final: 0.6706 (mtt-85) REVERT: A 347 ARG cc_start: 0.7741 (ptm160) cc_final: 0.7267 (ttp-110) REVERT: A 358 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 46 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7297 (mpp-170) REVERT: B 101 MET cc_start: 0.8500 (mtp) cc_final: 0.8104 (mtp) REVERT: B 252 LEU cc_start: 0.6072 (tt) cc_final: 0.5670 (tp) REVERT: M 51 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6980 (tpp80) REVERT: M 69 LEU cc_start: 0.8198 (mp) cc_final: 0.7871 (mm) REVERT: R 98 ILE cc_start: 0.7088 (tp) cc_final: 0.6851 (mm) REVERT: R 271 LEU cc_start: 0.8139 (mt) cc_final: 0.7871 (tp) outliers start: 27 outliers final: 17 residues processed: 147 average time/residue: 0.4921 time to fit residues: 77.8509 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.198947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164904 restraints weight = 10355.785| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.95 r_work: 0.3847 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8893 Z= 0.118 Angle : 0.545 10.029 12048 Z= 0.284 Chirality : 0.041 0.212 1370 Planarity : 0.004 0.044 1512 Dihedral : 4.297 27.578 1188 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.53 % Allowed : 15.93 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1069 helix: 2.36 (0.23), residues: 452 sheet: 0.43 (0.36), residues: 199 loop : -0.66 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 38 TYR 0.012 0.001 TYR A 37 PHE 0.024 0.001 PHE A 212 TRP 0.014 0.002 TRP A 234 HIS 0.014 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8889) covalent geometry : angle 0.54517 (12040) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.51149 ( 8) hydrogen bonds : bond 0.04330 ( 481) hydrogen bonds : angle 4.23352 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7425 (mtm110) cc_final: 0.6656 (mtt-85) REVERT: A 347 ARG cc_start: 0.7724 (ptm160) cc_final: 0.7255 (ttp-110) REVERT: A 358 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6879 (t80) REVERT: B 46 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7234 (mpp-170) REVERT: B 101 MET cc_start: 0.8507 (mtp) cc_final: 0.8108 (mtp) REVERT: B 252 LEU cc_start: 0.5989 (tt) cc_final: 0.5506 (tp) REVERT: M 51 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6930 (tpp80) REVERT: M 69 LEU cc_start: 0.8181 (mp) cc_final: 0.7859 (mm) REVERT: R 98 ILE cc_start: 0.7044 (tp) cc_final: 0.6822 (mm) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.4858 time to fit residues: 79.1566 Evaluate side-chains 145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.4306 r_free = 0.4306 target = 0.198757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166970 restraints weight = 10301.654| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.77 r_work: 0.3840 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8893 Z= 0.120 Angle : 0.565 10.046 12048 Z= 0.295 Chirality : 0.041 0.212 1370 Planarity : 0.004 0.052 1512 Dihedral : 4.267 27.873 1188 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 17.83 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1069 helix: 2.39 (0.23), residues: 452 sheet: 0.45 (0.36), residues: 198 loop : -0.68 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 256 TYR 0.013 0.001 TYR A 311 PHE 0.029 0.002 PHE M 53 TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8889) covalent geometry : angle 0.56454 (12040) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.55182 ( 8) hydrogen bonds : bond 0.04282 ( 481) hydrogen bonds : angle 4.21214 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.343 Fit side-chains REVERT: A 283 ARG cc_start: 0.7357 (mtm110) cc_final: 0.6618 (mtt-85) REVERT: A 347 ARG cc_start: 0.7743 (ptm160) cc_final: 0.7260 (ttp-110) REVERT: B 46 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7211 (mpp-170) REVERT: B 59 TYR cc_start: 0.7977 (m-80) cc_final: 0.7712 (m-80) REVERT: B 101 MET cc_start: 0.8500 (mtp) cc_final: 0.8076 (mtp) REVERT: B 252 LEU cc_start: 0.5981 (tt) cc_final: 0.5545 (tp) REVERT: M 51 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6944 (tpp80) REVERT: M 69 LEU cc_start: 0.8172 (mp) cc_final: 0.7860 (mm) REVERT: R 98 ILE cc_start: 0.7032 (tp) cc_final: 0.6821 (mm) outliers start: 21 outliers final: 17 residues processed: 143 average time/residue: 0.5035 time to fit residues: 77.2507 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.198905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167042 restraints weight = 10318.826| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.76 r_work: 0.3850 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8893 Z= 0.121 Angle : 0.557 9.725 12048 Z= 0.291 Chirality : 0.041 0.209 1370 Planarity : 0.004 0.061 1512 Dihedral : 4.264 26.938 1188 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 17.72 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1069 helix: 2.40 (0.23), residues: 452 sheet: 0.42 (0.36), residues: 198 loop : -0.67 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 256 TYR 0.013 0.001 TYR A 311 PHE 0.025 0.002 PHE A 212 TRP 0.015 0.002 TRP R 285 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8889) covalent geometry : angle 0.55743 (12040) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.58449 ( 8) hydrogen bonds : bond 0.04279 ( 481) hydrogen bonds : angle 4.19421 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.63 seconds wall clock time: 61 minutes 6.83 seconds (3666.83 seconds total)