Starting phenix.real_space_refine on Thu Jul 2 06:40:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy8_29560/07_2026/8fy8_29560.map" } resolution = 2.79 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= 0.037 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 P 2 5.49 5 S 54 5.16 5 C 4663 2.51 5 N 1236 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7309 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1891 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 143 Unusual residues: {'J40': 1, 'Y01': 2, 'YFW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.34, per 1000 atoms: 0.18 Number of scatterers: 7309 At special positions: 0 Unit cell: (74.244, 100.068, 129.12, 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) S 54 16.00 P 2 15.00 O 1354 8.00 N 1236 7.00 C 4663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 0.46 Conformation dependent library (CDL) restraints added in 284.0 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 47.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.568A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.066A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.199A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.623A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.504A pdb=" N CYS R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.693A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 183 removed outlier: 4.387A pdb=" N ARG R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 228 removed outlier: 5.708A pdb=" N ILE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix Processing helix chain 'R' and resid 325 through 371 Proline residue: R 360 - end of helix removed outlier: 3.659A pdb=" N VAL R 364 " --> pdb=" O PRO R 360 " (cutoff:3.500A) Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 378 through 391 Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.816A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.553A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.786A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.434A 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: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.523A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.296A 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: 6.448A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.902A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320 390 hydrogen bonds defined for protein. 1137 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: 0.97 Time building geometry restraints manager: 0.55 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: 1191 1.30 - 1.43: 1882 1.43 - 1.56: 4294 1.56 - 1.68: 9 1.68 - 1.81: 76 Bond restraints: 7452 Sorted by residual: bond pdb=" C VAL R 117 " pdb=" O VAL R 117 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.23e-02 6.61e+03 2.79e+01 bond pdb=" O4 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.702 1.614 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.24e-02 6.50e+03 1.73e+01 bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.07e-02 8.73e+03 1.65e+01 bond pdb=" N LEU R 359 " pdb=" CA LEU R 359 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 ... (remaining 7447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 9980 3.53 - 7.06: 109 7.06 - 10.60: 5 10.60 - 14.13: 0 14.13 - 17.66: 1 Bond angle restraints: 10095 Sorted by residual: angle pdb=" O1 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O13 J40 R 502 " ideal model delta sigma weight residual 92.86 110.52 -17.66 3.00e+00 1.11e-01 3.47e+01 angle pdb=" N ILE R 363 " pdb=" CA ILE R 363 " pdb=" C ILE R 363 " ideal model delta sigma weight residual 110.82 105.73 5.09 9.70e-01 1.06e+00 2.76e+01 angle pdb=" N ILE R 163 " pdb=" CA ILE R 163 " pdb=" C ILE R 163 " ideal model delta sigma weight residual 110.62 105.65 4.97 1.02e+00 9.61e-01 2.37e+01 angle pdb=" CA ILE B 58 " pdb=" C ILE B 58 " pdb=" O ILE B 58 " ideal model delta sigma weight residual 121.58 116.80 4.78 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N LEU B 336 " pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 110.32 102.92 7.40 1.59e+00 3.96e-01 2.17e+01 ... (remaining 10090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 4329 23.34 - 46.68: 234 46.68 - 70.02: 31 70.02 - 93.36: 5 93.36 - 116.70: 1 Dihedral angle restraints: 4600 sinusoidal: 1938 harmonic: 2662 Sorted by residual: dihedral pdb=" C40 J40 R 502 " pdb=" C41 J40 R 502 " pdb=" C42 J40 R 502 " pdb=" C43 J40 R 502 " ideal model delta sinusoidal sigma weight residual 178.73 62.03 116.70 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C HIS B 54 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " pdb=" CB HIS B 54 " ideal model delta harmonic sigma weight residual -122.60 -113.82 -8.78 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" CA ASP B 246 " pdb=" CB ASP B 246 " pdb=" CG ASP B 246 " pdb=" OD1 ASP B 246 " ideal model delta sinusoidal sigma weight residual -30.00 -87.62 57.62 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 801 0.047 - 0.094: 231 0.094 - 0.142: 92 0.142 - 0.189: 25 0.189 - 0.236: 11 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA LEU B 336 " pdb=" N LEU B 336 " pdb=" C LEU B 336 " pdb=" CB LEU B 336 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE R 363 " pdb=" N ILE R 363 " pdb=" C ILE R 363 " pdb=" CB ILE R 363 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1157 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YFW R 501 " -0.036 2.00e-02 2.50e+03 3.68e-02 3.72e+01 pdb=" O YFW R 501 " -0.070 2.00e-02 2.50e+03 pdb=" C1 YFW R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C11 YFW R 501 " 0.021 2.00e-02 2.50e+03 pdb=" C12 YFW R 501 " 0.015 2.00e-02 2.50e+03 pdb=" C2 YFW R 501 " 0.030 2.00e-02 2.50e+03 pdb=" C3 YFW R 501 " 0.037 2.00e-02 2.50e+03 pdb=" C4 YFW R 501 " 0.018 2.00e-02 2.50e+03 pdb=" C5 YFW R 501 " -0.058 2.00e-02 2.50e+03 pdb=" C6 YFW R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C7 YFW R 501 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 79 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LEU B 79 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU B 79 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 80 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 197 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C LYS A 197 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 197 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 198 " 0.018 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2121 2.83 - 3.34: 7051 3.34 - 3.86: 12434 3.86 - 4.38: 14373 4.38 - 4.90: 25105 Nonbonded interactions: 61084 Sorted by model distance: nonbonded pdb=" O LEU R 166 " pdb=" OH TYR R 198 " model vdw 2.307 3.040 nonbonded pdb=" NE ARG R 227 " pdb=" OE2 GLU R 340 " model vdw 2.323 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.327 3.040 nonbonded pdb=" O LEU R 173 " pdb=" CD1 LEU R 173 " model vdw 2.335 3.460 nonbonded pdb=" OD1 ASN B 340 " pdb=" ND2 ASN G 59 " model vdw 2.375 3.120 ... (remaining 61079 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: 1.110 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.007 0.088 7453 Z= 0.494 Angle : 0.953 17.660 10097 Z= 0.641 Chirality : 0.057 0.236 1160 Planarity : 0.005 0.037 1262 Dihedral : 13.633 116.703 2869 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.13 % Allowed : 1.68 % Favored : 98.20 % 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: 0.09 (0.28), residues: 902 helix: 1.41 (0.26), residues: 412 sheet: -0.84 (0.36), residues: 192 loop : -1.15 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.015 0.002 TYR B 124 PHE 0.011 0.002 PHE B 235 TRP 0.016 0.001 TRP R 387 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.49 ( 7452) covalent geometry : angle 0.95321 / 0.64 (10095) SS BOND : bond 0.00214 / 0.11 ( 1) SS BOND : angle 0.12823 / 0.06 ( 2) hydrogen bonds : bond 0.15465 / 10.71 ( 390) hydrogen bonds : angle 6.66686 / 4.77 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.172 Fit side-chains REVERT: A 341 ASP cc_start: 0.8209 (t0) cc_final: 0.8004 (t0) REVERT: B 59 TYR cc_start: 0.7699 (m-80) cc_final: 0.7420 (m-80) REVERT: B 226 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 298 ASP cc_start: 0.8356 (t70) cc_final: 0.8098 (t70) REVERT: G 46 LYS cc_start: 0.8560 (tptt) cc_final: 0.8218 (tppt) REVERT: R 356 LEU cc_start: 0.7962 (tp) cc_final: 0.7572 (mm) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.3582 time to fit residues: 46.8607 Evaluate side-chains 101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096895 restraints weight = 8014.954| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.62 r_work: 0.3050 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7453 Z= 0.142 Angle : 0.541 8.844 10097 Z= 0.276 Chirality : 0.043 0.192 1160 Planarity : 0.004 0.039 1262 Dihedral : 8.989 89.857 1208 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.16 % Allowed : 8.51 % Favored : 90.34 % 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: 0.84 (0.28), residues: 902 helix: 2.21 (0.26), residues: 407 sheet: -0.48 (0.38), residues: 175 loop : -1.01 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.010 0.001 TYR R 195 PHE 0.009 0.001 PHE A 196 TRP 0.022 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7452) covalent geometry : angle 0.54121 / 0.28 (10095) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.14550 / 0.09 ( 2) hydrogen bonds : bond 0.04194 / 2.88 ( 390) hydrogen bonds : angle 4.81563 / 3.43 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.182 Fit side-chains REVERT: B 226 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 46 LYS cc_start: 0.8413 (tptt) cc_final: 0.7964 (tppt) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 0.3247 time to fit residues: 34.2072 Evaluate side-chains 82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.091675 restraints weight = 7838.044| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.85 r_work: 0.3031 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7453 Z= 0.160 Angle : 0.537 7.562 10097 Z= 0.273 Chirality : 0.043 0.187 1160 Planarity : 0.004 0.039 1262 Dihedral : 8.626 89.438 1208 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.68 % Allowed : 10.82 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 902 helix: 2.33 (0.25), residues: 407 sheet: -0.64 (0.37), residues: 180 loop : -0.96 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.010 0.001 TYR R 195 PHE 0.014 0.002 PHE R 407 TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 7452) covalent geometry : angle 0.53659 / 0.27 (10095) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.24857 / 0.15 ( 2) hydrogen bonds : bond 0.03878 / 2.67 ( 390) hydrogen bonds : angle 4.56473 / 3.24 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.265 Fit side-chains REVERT: A 253 ILE cc_start: 0.8150 (tp) cc_final: 0.7892 (tp) REVERT: B 45 MET cc_start: 0.8218 (mtt) cc_final: 0.7996 (mtt) REVERT: B 59 TYR cc_start: 0.8616 (m-80) cc_final: 0.8396 (m-80) REVERT: B 226 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 298 ASP cc_start: 0.8769 (t70) cc_final: 0.8345 (t70) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.3140 time to fit residues: 32.5981 Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099813 restraints weight = 7741.524| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.73 r_work: 0.3039 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7453 Z= 0.152 Angle : 0.522 7.457 10097 Z= 0.266 Chirality : 0.043 0.182 1160 Planarity : 0.004 0.039 1262 Dihedral : 8.521 89.751 1208 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 11.47 % Favored : 87.24 % 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: 0.92 (0.28), residues: 902 helix: 2.39 (0.25), residues: 406 sheet: -0.63 (0.38), residues: 180 loop : -0.99 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.010 0.001 TYR R 195 PHE 0.012 0.002 PHE R 407 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 7452) covalent geometry : angle 0.52158 / 0.27 (10095) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.19785 / 0.11 ( 2) hydrogen bonds : bond 0.03715 / 2.56 ( 390) hydrogen bonds : angle 4.44668 / 3.15 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.272 Fit side-chains REVERT: A 197 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7846 (mtmt) REVERT: A 253 ILE cc_start: 0.8137 (tp) cc_final: 0.7809 (tp) REVERT: B 226 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.3455 time to fit residues: 34.9872 Evaluate side-chains 90 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.0370 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100950 restraints weight = 7617.635| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.68 r_work: 0.2860 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7453 Z= 0.132 Angle : 0.505 7.586 10097 Z= 0.259 Chirality : 0.042 0.177 1160 Planarity : 0.003 0.038 1262 Dihedral : 8.433 88.847 1208 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 12.63 % Favored : 85.95 % 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: 1.00 (0.28), residues: 902 helix: 2.50 (0.25), residues: 404 sheet: -0.63 (0.38), residues: 180 loop : -0.98 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.009 0.001 TYR R 195 PHE 0.010 0.001 PHE A 189 TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7452) covalent geometry : angle 0.50478 / 0.26 (10095) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.13763 / 0.08 ( 2) hydrogen bonds : bond 0.03558 / 2.45 ( 390) hydrogen bonds : angle 4.36898 / 3.09 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.247 Fit side-chains REVERT: A 197 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7322 (mtmt) REVERT: A 253 ILE cc_start: 0.7623 (tp) cc_final: 0.7306 (tp) REVERT: B 45 MET cc_start: 0.8072 (mtt) cc_final: 0.7758 (mtt) REVERT: B 226 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7663 (mt-10) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.3345 time to fit residues: 31.2697 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101813 restraints weight = 7631.284| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.67 r_work: 0.2887 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7453 Z= 0.121 Angle : 0.500 8.312 10097 Z= 0.255 Chirality : 0.041 0.176 1160 Planarity : 0.003 0.037 1262 Dihedral : 8.350 88.815 1208 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.55 % Allowed : 13.27 % Favored : 85.18 % 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: 1.02 (0.28), residues: 902 helix: 2.51 (0.25), residues: 405 sheet: -0.71 (0.38), residues: 185 loop : -0.91 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.009 0.001 TYR R 195 PHE 0.009 0.001 PHE A 189 TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7452) covalent geometry : angle 0.50035 / 0.26 (10095) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 0.10021 / 0.06 ( 2) hydrogen bonds : bond 0.03476 / 2.39 ( 390) hydrogen bonds : angle 4.30457 / 3.05 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.313 Fit side-chains REVERT: A 197 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7326 (mtmt) REVERT: A 253 ILE cc_start: 0.7696 (tp) cc_final: 0.7374 (tp) REVERT: B 45 MET cc_start: 0.8117 (mtt) cc_final: 0.7837 (mtt) REVERT: B 226 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7650 (mt-10) REVERT: R 159 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6763 (tm) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.3670 time to fit residues: 35.1520 Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097793 restraints weight = 7668.250| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.67 r_work: 0.3012 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7453 Z= 0.202 Angle : 0.561 8.652 10097 Z= 0.287 Chirality : 0.044 0.176 1160 Planarity : 0.004 0.039 1262 Dihedral : 8.564 89.604 1208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.55 % Allowed : 13.79 % Favored : 84.66 % 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: 0.79 (0.28), residues: 902 helix: 2.26 (0.25), residues: 410 sheet: -0.73 (0.38), residues: 185 loop : -1.06 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.013 0.002 TYR B 59 PHE 0.012 0.002 PHE A 223 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 7452) covalent geometry : angle 0.56084 / 0.29 (10095) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 0.23264 / 0.13 ( 2) hydrogen bonds : bond 0.03909 / 2.71 ( 390) hydrogen bonds : angle 4.49495 / 3.17 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.246 Fit side-chains REVERT: B 226 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 237 ASN cc_start: 0.7895 (t0) cc_final: 0.7597 (t0) REVERT: R 159 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7144 (tm) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.3076 time to fit residues: 31.7888 Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099998 restraints weight = 7635.659| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.67 r_work: 0.3042 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7453 Z= 0.141 Angle : 0.513 7.609 10097 Z= 0.264 Chirality : 0.042 0.175 1160 Planarity : 0.003 0.039 1262 Dihedral : 8.365 89.274 1208 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 14.05 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 902 helix: 2.36 (0.25), residues: 410 sheet: -0.71 (0.38), residues: 185 loop : -1.02 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.009 0.001 TYR R 195 PHE 0.010 0.001 PHE A 189 TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7452) covalent geometry : angle 0.51326 / 0.26 (10095) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 0.16864 / 0.10 ( 2) hydrogen bonds : bond 0.03605 / 2.48 ( 390) hydrogen bonds : angle 4.39296 / 3.11 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.196 Fit side-chains REVERT: A 197 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7759 (mtmt) REVERT: B 45 MET cc_start: 0.8338 (mtt) cc_final: 0.7948 (mtt) REVERT: B 226 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 298 ASP cc_start: 0.8604 (t70) cc_final: 0.8239 (t70) REVERT: R 159 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7176 (tm) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.3329 time to fit residues: 31.2669 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100694 restraints weight = 7588.741| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.67 r_work: 0.2857 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7453 Z= 0.130 Angle : 0.503 7.705 10097 Z= 0.257 Chirality : 0.042 0.176 1160 Planarity : 0.003 0.038 1262 Dihedral : 8.276 89.183 1208 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 14.69 % Favored : 83.89 % 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: 0.96 (0.28), residues: 902 helix: 2.45 (0.25), residues: 410 sheet: -0.70 (0.38), residues: 185 loop : -1.00 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.009 0.001 TYR R 195 PHE 0.010 0.001 PHE A 189 TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7452) covalent geometry : angle 0.50255 / 0.26 (10095) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.20444 / 0.12 ( 2) hydrogen bonds : bond 0.03499 / 2.41 ( 390) hydrogen bonds : angle 4.34243 / 3.07 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.301 Fit side-chains REVERT: A 197 LYS cc_start: 0.7455 (mtpp) cc_final: 0.7202 (mtmt) REVERT: B 45 MET cc_start: 0.8136 (mtt) cc_final: 0.7756 (mtt) REVERT: B 226 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7560 (mt-10) REVERT: R 101 LYS cc_start: 0.7236 (pttt) cc_final: 0.6832 (ptpt) REVERT: R 159 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6622 (tm) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.3366 time to fit residues: 30.0032 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100488 restraints weight = 7623.666| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.67 r_work: 0.3051 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7453 Z= 0.138 Angle : 0.509 7.320 10097 Z= 0.261 Chirality : 0.042 0.176 1160 Planarity : 0.003 0.037 1262 Dihedral : 8.287 89.426 1208 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 14.95 % Favored : 83.76 % 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: 0.96 (0.28), residues: 902 helix: 2.44 (0.25), residues: 410 sheet: -0.69 (0.39), residues: 185 loop : -1.00 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.010 0.001 TYR R 195 PHE 0.010 0.001 PHE A 196 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7452) covalent geometry : angle 0.50893 / 0.26 (10095) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.20864 / 0.12 ( 2) hydrogen bonds : bond 0.03515 / 2.42 ( 390) hydrogen bonds : angle 4.33846 / 3.07 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.222 Fit side-chains REVERT: A 197 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7763 (mtmt) REVERT: B 45 MET cc_start: 0.8346 (mtt) cc_final: 0.7963 (mtt) REVERT: B 226 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 298 ASP cc_start: 0.8536 (t70) cc_final: 0.8264 (t70) REVERT: R 101 LYS cc_start: 0.7815 (pttt) cc_final: 0.7400 (ptpt) REVERT: R 159 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7196 (tm) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.3062 time to fit residues: 27.1363 Evaluate side-chains 82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099741 restraints weight = 7563.315| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.64 r_work: 0.2845 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7453 Z= 0.158 Angle : 0.519 7.530 10097 Z= 0.266 Chirality : 0.043 0.177 1160 Planarity : 0.003 0.038 1262 Dihedral : 8.333 89.901 1208 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.29 % Allowed : 14.82 % Favored : 83.89 % 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: 0.92 (0.28), residues: 902 helix: 2.40 (0.25), residues: 410 sheet: -0.71 (0.39), residues: 185 loop : -0.99 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.001 PHE A 196 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7452) covalent geometry : angle 0.51905 / 0.27 (10095) SS BOND : bond 0.00119 / 0.06 ( 1) SS BOND : angle 0.25000 / 0.14 ( 2) hydrogen bonds : bond 0.03604 / 2.48 ( 390) hydrogen bonds : angle 4.37334 / 3.09 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.48 seconds wall clock time: 33 minutes 15.66 seconds (1995.66 seconds total)