Starting phenix.real_space_refine on Sun Apr 5 05:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1p_63579/04_2026/9m1p_63579.map" } resolution = 2.8 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= 0.002 sd= 0.031 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 61 5.16 5 C 5375 2.51 5 N 1453 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8461 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2524 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 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: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "A" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1926 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.23 Number of scatterers: 8461 At special positions: 0 Unit cell: (76.544, 99.008, 138.112, 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 61 16.00 O 1572 8.00 N 1453 7.00 C 5375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 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 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: 0.63 Conformation dependent library (CDL) restraints added in 319.2 milliseconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 43.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 85 Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.829A pdb=" N ILE R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 177 through 184 Processing helix chain 'R' and resid 195 through 233 removed outlier: 4.483A pdb=" N LEU R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) Proline residue: R 210 - end of helix Processing helix chain 'R' and resid 250 through 279 removed outlier: 3.936A pdb=" N PHE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 280 through 283 removed outlier: 3.808A pdb=" N ASN R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 280 through 283' Processing helix chain 'R' and resid 287 through 309 removed outlier: 3.626A pdb=" N SER R 302 " --> pdb=" O GLY R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 removed outlier: 3.514A pdb=" N ARG R 317 " --> pdb=" O TYR R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 330 Processing helix chain 'R' and resid 332 through 336 removed outlier: 3.656A pdb=" N ASP R 335 " --> pdb=" O ASN R 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 332 through 336' Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.511A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.595A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 36 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.901A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.652A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.972A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.820A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.129A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.528A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.491A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.465A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.075A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.703A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.798A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.695A pdb=" N VAL A 86 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASP A 111 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1266 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: 1.10 Time building geometry restraints manager: 0.89 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: 2736 1.34 - 1.46: 1571 1.46 - 1.57: 4247 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8644 Sorted by residual: bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.488 -0.028 7.50e-03 1.78e+04 1.43e+01 bond pdb=" N ILE R 155 " pdb=" CA ILE R 155 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.30e-02 5.92e+03 9.98e+00 bond pdb=" N ARG A 169 " pdb=" CA ARG A 169 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.10e-02 8.26e+03 8.57e+00 bond pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.32e-02 5.74e+03 8.54e+00 bond pdb=" N TYR R 100 " pdb=" CA TYR R 100 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.45e+00 ... (remaining 8639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11337 1.60 - 3.20: 338 3.20 - 4.80: 36 4.80 - 6.41: 3 6.41 - 8.01: 4 Bond angle restraints: 11718 Sorted by residual: angle pdb=" N ARG A 199 " pdb=" CA ARG A 199 " pdb=" C ARG A 199 " ideal model delta sigma weight residual 111.07 106.96 4.11 1.07e+00 8.73e-01 1.48e+01 angle pdb=" C ALA B 92 " pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 122.59 119.96 2.63 7.20e-01 1.93e+00 1.34e+01 angle pdb=" CA ARG B 49 " pdb=" C ARG B 49 " pdb=" O ARG B 49 " ideal model delta sigma weight residual 120.70 117.23 3.47 1.08e+00 8.57e-01 1.03e+01 angle pdb=" CA LEU B 308 " pdb=" C LEU B 308 " pdb=" O LEU B 308 " ideal model delta sigma weight residual 122.51 118.24 4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" O ILE B 58 " pdb=" C ILE B 58 " pdb=" N TYR B 59 " ideal model delta sigma weight residual 123.14 126.34 -3.20 1.02e+00 9.61e-01 9.83e+00 ... (remaining 11713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 4672 16.88 - 33.76: 361 33.76 - 50.64: 70 50.64 - 67.52: 23 67.52 - 84.41: 9 Dihedral angle restraints: 5135 sinusoidal: 2009 harmonic: 3126 Sorted by residual: dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -149.24 63.24 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CD ARG A 94 " pdb=" NE ARG A 94 " pdb=" CZ ARG A 94 " pdb=" NH1 ARG A 94 " ideal model delta sinusoidal sigma weight residual 0.00 -41.36 41.36 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CD ARG B 48 " pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " pdb=" NH1 ARG B 48 " ideal model delta sinusoidal sigma weight residual 0.00 -40.47 40.47 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 942 0.045 - 0.089: 280 0.089 - 0.134: 81 0.134 - 0.178: 11 0.178 - 0.223: 4 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL B 158 " pdb=" N VAL B 158 " pdb=" C VAL B 158 " pdb=" CB VAL B 158 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1315 not shown) Planarity restraints: 1493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " 0.707 9.50e-02 1.11e+02 3.17e-01 6.12e+01 pdb=" NE ARG A 94 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 48 " 0.697 9.50e-02 1.11e+02 3.12e-01 5.95e+01 pdb=" NE ARG B 48 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 48 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 48 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 48 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " 0.453 9.50e-02 1.11e+02 2.03e-01 2.53e+01 pdb=" NE ARG A 188 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " 0.015 2.00e-02 2.50e+03 ... (remaining 1490 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 500 2.73 - 3.27: 8486 3.27 - 3.82: 14679 3.82 - 4.36: 17787 4.36 - 4.90: 30696 Nonbonded interactions: 72148 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.188 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR R 67 " pdb=" OD2 ASP R 129 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.323 3.040 ... (remaining 72143 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: 1.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8649 Z= 0.248 Angle : 0.609 8.008 11728 Z= 0.376 Chirality : 0.047 0.223 1318 Planarity : 0.015 0.317 1493 Dihedral : 13.201 84.406 3100 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 (0.26), residues: 1059 helix: 1.96 (0.26), residues: 424 sheet: 0.14 (0.33), residues: 216 loop : -0.30 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 94 TYR 0.020 0.001 TYR R 36 PHE 0.012 0.001 PHE R 114 TRP 0.013 0.001 TRP A 96 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8644) covalent geometry : angle 0.60897 (11718) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.92382 ( 10) hydrogen bonds : bond 0.16826 ( 444) hydrogen bonds : angle 6.57238 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.279 Fit side-chains REVERT: R 38 ILE cc_start: 0.8593 (tp) cc_final: 0.8316 (tp) REVERT: R 282 ILE cc_start: 0.7890 (tt) cc_final: 0.7671 (tp) REVERT: B 25 CYS cc_start: 0.7242 (m) cc_final: 0.6880 (m) REVERT: B 52 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6851 (ttp-170) REVERT: B 217 MET cc_start: 0.6609 (ppp) cc_final: 0.6361 (ppp) REVERT: B 256 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7602 (mtm180) REVERT: B 258 ASP cc_start: 0.6792 (t70) cc_final: 0.6354 (t0) REVERT: B 320 VAL cc_start: 0.8471 (t) cc_final: 0.8253 (m) REVERT: N 57 SER cc_start: 0.7733 (m) cc_final: 0.7447 (m) REVERT: A 12 SER cc_start: 0.8352 (p) cc_final: 0.7243 (p) REVERT: A 14 GLU cc_start: 0.7141 (pm20) cc_final: 0.6771 (pm20) REVERT: A 23 LYS cc_start: 0.7632 (tttp) cc_final: 0.7386 (tttp) REVERT: A 144 ASN cc_start: 0.7929 (t0) cc_final: 0.7638 (t160) outliers start: 0 outliers final: 1 residues processed: 224 average time/residue: 0.5033 time to fit residues: 120.6825 Evaluate side-chains 198 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 230 ASN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114635 restraints weight = 11766.966| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.88 r_work: 0.3426 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8649 Z= 0.179 Angle : 0.528 6.994 11728 Z= 0.286 Chirality : 0.044 0.141 1318 Planarity : 0.004 0.042 1493 Dihedral : 4.427 41.656 1174 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.07 % Allowed : 9.90 % Favored : 88.03 % 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: 1.05 (0.26), residues: 1059 helix: 1.98 (0.25), residues: 425 sheet: 0.08 (0.32), residues: 229 loop : -0.25 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 117 TYR 0.015 0.001 TYR R 36 PHE 0.014 0.001 PHE R 15 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8644) covalent geometry : angle 0.52735 (11718) SS BOND : bond 0.00425 ( 5) SS BOND : angle 0.95656 ( 10) hydrogen bonds : bond 0.04411 ( 444) hydrogen bonds : angle 5.10197 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.293 Fit side-chains REVERT: R 38 ILE cc_start: 0.8638 (tp) cc_final: 0.8382 (tp) REVERT: R 282 ILE cc_start: 0.8224 (tt) cc_final: 0.7878 (tp) REVERT: B 25 CYS cc_start: 0.8180 (m) cc_final: 0.7811 (m) REVERT: B 212 ASP cc_start: 0.8007 (t0) cc_final: 0.7549 (t0) REVERT: B 217 MET cc_start: 0.7808 (ppp) cc_final: 0.7447 (ppp) REVERT: B 219 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7613 (mmt90) REVERT: B 251 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8137 (mtt-85) REVERT: B 256 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7877 (mtp180) REVERT: B 258 ASP cc_start: 0.7433 (t70) cc_final: 0.6880 (t0) REVERT: N 76 LYS cc_start: 0.8699 (mppt) cc_final: 0.8499 (mtmm) REVERT: A 20 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 23 LYS cc_start: 0.8089 (tttp) cc_final: 0.7853 (tttp) outliers start: 19 outliers final: 8 residues processed: 211 average time/residue: 0.5142 time to fit residues: 116.1486 Evaluate side-chains 194 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN A 80 ASN A 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.127392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114447 restraints weight = 11718.827| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.85 r_work: 0.3431 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8649 Z= 0.157 Angle : 0.505 7.654 11728 Z= 0.271 Chirality : 0.043 0.143 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.220 42.032 1172 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.05 % Allowed : 12.73 % Favored : 84.22 % 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: 1.03 (0.26), residues: 1059 helix: 2.02 (0.26), residues: 425 sheet: 0.02 (0.32), residues: 229 loop : -0.28 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.020 0.001 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8644) covalent geometry : angle 0.50410 (11718) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.96546 ( 10) hydrogen bonds : bond 0.04138 ( 444) hydrogen bonds : angle 4.90434 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.304 Fit side-chains REVERT: R 38 ILE cc_start: 0.8652 (tp) cc_final: 0.8409 (tp) REVERT: R 282 ILE cc_start: 0.8214 (tt) cc_final: 0.7878 (tp) REVERT: B 25 CYS cc_start: 0.8186 (m) cc_final: 0.7812 (m) REVERT: B 188 MET cc_start: 0.8108 (mmm) cc_final: 0.7786 (mmm) REVERT: B 212 ASP cc_start: 0.8015 (t0) cc_final: 0.7568 (t0) REVERT: B 217 MET cc_start: 0.7805 (ppp) cc_final: 0.7473 (ppp) REVERT: B 219 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.7651 (mmt90) REVERT: B 251 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8193 (mtt-85) REVERT: B 256 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7907 (mtm180) REVERT: B 258 ASP cc_start: 0.7404 (t70) cc_final: 0.6766 (t0) REVERT: C 42 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 20 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 23 LYS cc_start: 0.8042 (tttp) cc_final: 0.7801 (tttp) REVERT: A 80 ASN cc_start: 0.8233 (m110) cc_final: 0.7943 (m110) outliers start: 28 outliers final: 13 residues processed: 201 average time/residue: 0.5159 time to fit residues: 110.9054 Evaluate side-chains 205 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 301 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114322 restraints weight = 11952.473| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.87 r_work: 0.3421 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8649 Z= 0.162 Angle : 0.494 6.061 11728 Z= 0.267 Chirality : 0.043 0.136 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.202 42.518 1172 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.94 % Allowed : 13.82 % Favored : 83.24 % 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: 1.05 (0.27), residues: 1059 helix: 2.08 (0.26), residues: 420 sheet: 0.06 (0.32), residues: 229 loop : -0.31 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.015 0.001 TYR R 180 PHE 0.017 0.001 PHE R 13 TRP 0.016 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8644) covalent geometry : angle 0.49303 (11718) SS BOND : bond 0.00331 ( 5) SS BOND : angle 0.91562 ( 10) hydrogen bonds : bond 0.03977 ( 444) hydrogen bonds : angle 4.82765 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.215 Fit side-chains REVERT: R 38 ILE cc_start: 0.8654 (tp) cc_final: 0.8412 (tp) REVERT: R 282 ILE cc_start: 0.8224 (tt) cc_final: 0.7881 (tp) REVERT: B 25 CYS cc_start: 0.8130 (m) cc_final: 0.7755 (m) REVERT: B 212 ASP cc_start: 0.8045 (t0) cc_final: 0.7608 (t0) REVERT: B 217 MET cc_start: 0.7805 (ppp) cc_final: 0.7503 (ppp) REVERT: B 251 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8216 (ttm170) REVERT: B 256 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7838 (mtm180) REVERT: B 258 ASP cc_start: 0.7446 (t70) cc_final: 0.6840 (t0) REVERT: B 325 MET cc_start: 0.8817 (tpp) cc_final: 0.8566 (tpt) REVERT: C 42 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 23 LYS cc_start: 0.8083 (tttp) cc_final: 0.7851 (tttp) outliers start: 27 outliers final: 16 residues processed: 207 average time/residue: 0.5488 time to fit residues: 120.9349 Evaluate side-chains 204 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113890 restraints weight = 11886.906| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.87 r_work: 0.3416 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8649 Z= 0.186 Angle : 0.517 8.487 11728 Z= 0.275 Chirality : 0.043 0.140 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.244 44.088 1172 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.26 % Allowed : 14.04 % Favored : 82.70 % 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 (0.27), residues: 1059 helix: 2.01 (0.26), residues: 420 sheet: -0.02 (0.33), residues: 230 loop : -0.35 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.015 0.001 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.016 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8644) covalent geometry : angle 0.51616 (11718) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.94021 ( 10) hydrogen bonds : bond 0.04062 ( 444) hydrogen bonds : angle 4.84758 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.343 Fit side-chains REVERT: R 38 ILE cc_start: 0.8655 (tp) cc_final: 0.8413 (tp) REVERT: R 282 ILE cc_start: 0.8207 (tt) cc_final: 0.7856 (tp) REVERT: B 25 CYS cc_start: 0.8144 (m) cc_final: 0.7768 (m) REVERT: B 52 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7945 (ttp-170) REVERT: B 212 ASP cc_start: 0.8054 (t0) cc_final: 0.7548 (t0) REVERT: B 217 MET cc_start: 0.7779 (ppp) cc_final: 0.7407 (ppp) REVERT: B 219 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7661 (ttm170) REVERT: B 251 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8223 (ttm170) REVERT: B 258 ASP cc_start: 0.7614 (t70) cc_final: 0.6976 (t0) REVERT: B 304 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8226 (ttp-170) REVERT: B 325 MET cc_start: 0.8796 (tpp) cc_final: 0.8571 (tpt) REVERT: A 23 LYS cc_start: 0.8080 (tttp) cc_final: 0.7845 (tttp) REVERT: A 80 ASN cc_start: 0.8245 (m110) cc_final: 0.7911 (m110) REVERT: A 195 ASP cc_start: 0.8100 (m-30) cc_final: 0.7837 (m-30) REVERT: A 232 ARG cc_start: 0.8249 (ttp80) cc_final: 0.8026 (ttp-110) outliers start: 30 outliers final: 19 residues processed: 208 average time/residue: 0.5286 time to fit residues: 117.4689 Evaluate side-chains 213 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 A 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113204 restraints weight = 11630.617| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.86 r_work: 0.3409 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8649 Z= 0.217 Angle : 0.530 9.142 11728 Z= 0.283 Chirality : 0.045 0.160 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.328 46.860 1172 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.35 % Allowed : 14.04 % Favored : 81.61 % 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: 0.93 (0.27), residues: 1059 helix: 1.96 (0.26), residues: 420 sheet: -0.00 (0.34), residues: 224 loop : -0.34 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.014 0.001 TYR R 180 PHE 0.019 0.001 PHE R 13 TRP 0.017 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 8644) covalent geometry : angle 0.52979 (11718) SS BOND : bond 0.00402 ( 5) SS BOND : angle 1.02530 ( 10) hydrogen bonds : bond 0.04180 ( 444) hydrogen bonds : angle 4.86984 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.329 Fit side-chains REVERT: R 38 ILE cc_start: 0.8664 (tp) cc_final: 0.8441 (tp) REVERT: R 206 THR cc_start: 0.8249 (p) cc_final: 0.8039 (t) REVERT: R 282 ILE cc_start: 0.8257 (tt) cc_final: 0.7904 (tp) REVERT: B 25 CYS cc_start: 0.8146 (m) cc_final: 0.7779 (m) REVERT: B 52 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7894 (ttp-170) REVERT: B 212 ASP cc_start: 0.8044 (t0) cc_final: 0.7593 (t0) REVERT: B 217 MET cc_start: 0.7689 (ppp) cc_final: 0.7256 (ppp) REVERT: B 219 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7684 (ttm170) REVERT: B 251 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8191 (mtt-85) REVERT: B 258 ASP cc_start: 0.7642 (t70) cc_final: 0.6983 (t0) REVERT: B 304 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8283 (ttp-170) REVERT: A 23 LYS cc_start: 0.8067 (tttp) cc_final: 0.7826 (tttp) REVERT: A 95 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8285 (mptp) REVERT: A 148 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8154 (mt) REVERT: A 232 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7995 (ttp-110) outliers start: 40 outliers final: 22 residues processed: 205 average time/residue: 0.5128 time to fit residues: 112.3787 Evaluate side-chains 215 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN A 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114548 restraints weight = 11917.029| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.88 r_work: 0.3424 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8649 Z= 0.138 Angle : 0.510 8.688 11728 Z= 0.269 Chirality : 0.043 0.148 1318 Planarity : 0.004 0.040 1493 Dihedral : 4.173 45.960 1172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.26 % Allowed : 15.67 % Favored : 81.07 % 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: 1.09 (0.27), residues: 1059 helix: 2.09 (0.26), residues: 420 sheet: 0.09 (0.34), residues: 214 loop : -0.26 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 21 TYR 0.016 0.001 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.016 0.002 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8644) covalent geometry : angle 0.50931 (11718) SS BOND : bond 0.00277 ( 5) SS BOND : angle 0.86477 ( 10) hydrogen bonds : bond 0.03810 ( 444) hydrogen bonds : angle 4.75341 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.287 Fit side-chains REVERT: R 38 ILE cc_start: 0.8635 (tp) cc_final: 0.8414 (tp) REVERT: R 114 PHE cc_start: 0.8416 (t80) cc_final: 0.8198 (t80) REVERT: R 282 ILE cc_start: 0.8212 (tt) cc_final: 0.7858 (tp) REVERT: B 25 CYS cc_start: 0.8134 (m) cc_final: 0.7757 (m) REVERT: B 212 ASP cc_start: 0.8065 (t0) cc_final: 0.7544 (t0) REVERT: B 217 MET cc_start: 0.7753 (ppp) cc_final: 0.7331 (ppp) REVERT: B 219 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7673 (ttm170) REVERT: B 251 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8160 (mtt-85) REVERT: B 258 ASP cc_start: 0.7605 (t70) cc_final: 0.7137 (t0) REVERT: B 304 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8261 (mtm180) REVERT: A 23 LYS cc_start: 0.8063 (tttp) cc_final: 0.7816 (tttp) REVERT: A 80 ASN cc_start: 0.8219 (m110) cc_final: 0.7883 (m110) REVERT: A 148 LEU cc_start: 0.8491 (mp) cc_final: 0.8200 (mt) REVERT: A 195 ASP cc_start: 0.8096 (m-30) cc_final: 0.7877 (m-30) REVERT: A 232 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7993 (ttp-110) outliers start: 30 outliers final: 16 residues processed: 205 average time/residue: 0.5137 time to fit residues: 112.5708 Evaluate side-chains 205 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113934 restraints weight = 11764.838| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.87 r_work: 0.3411 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8649 Z= 0.191 Angle : 0.522 8.566 11728 Z= 0.277 Chirality : 0.044 0.151 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.249 47.002 1172 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.83 % Allowed : 16.21 % Favored : 80.96 % 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: 1.01 (0.27), residues: 1059 helix: 2.01 (0.26), residues: 420 sheet: 0.08 (0.34), residues: 209 loop : -0.31 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.015 0.001 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.016 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8644) covalent geometry : angle 0.52107 (11718) SS BOND : bond 0.00371 ( 5) SS BOND : angle 0.94804 ( 10) hydrogen bonds : bond 0.04003 ( 444) hydrogen bonds : angle 4.76479 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.307 Fit side-chains REVERT: R 38 ILE cc_start: 0.8655 (tp) cc_final: 0.8431 (tp) REVERT: R 282 ILE cc_start: 0.8237 (tt) cc_final: 0.7878 (tp) REVERT: B 25 CYS cc_start: 0.8151 (m) cc_final: 0.7778 (m) REVERT: B 212 ASP cc_start: 0.8057 (t0) cc_final: 0.7541 (t0) REVERT: B 217 MET cc_start: 0.7714 (ppp) cc_final: 0.7302 (ppp) REVERT: B 219 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7659 (ttm170) REVERT: B 251 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8180 (mtt-85) REVERT: B 258 ASP cc_start: 0.7655 (t70) cc_final: 0.6977 (t0) REVERT: B 304 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8296 (mtm180) REVERT: A 23 LYS cc_start: 0.8084 (tttp) cc_final: 0.7842 (tttp) REVERT: A 148 LEU cc_start: 0.8508 (mp) cc_final: 0.8217 (mt) REVERT: A 154 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8190 (mm) REVERT: A 195 ASP cc_start: 0.8105 (m-30) cc_final: 0.7863 (m-30) REVERT: A 232 ARG cc_start: 0.8220 (ttp80) cc_final: 0.8000 (ttp-110) outliers start: 26 outliers final: 18 residues processed: 202 average time/residue: 0.5265 time to fit residues: 113.5893 Evaluate side-chains 212 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN A 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114979 restraints weight = 11823.522| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.87 r_work: 0.3429 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8649 Z= 0.132 Angle : 0.511 9.053 11728 Z= 0.267 Chirality : 0.042 0.150 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.139 45.336 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.96 % Allowed : 17.30 % Favored : 80.74 % 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: 1.19 (0.27), residues: 1059 helix: 2.20 (0.26), residues: 414 sheet: 0.04 (0.34), residues: 214 loop : -0.13 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.016 0.001 TYR R 180 PHE 0.017 0.001 PHE R 13 TRP 0.017 0.002 TRP A 96 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8644) covalent geometry : angle 0.51027 (11718) SS BOND : bond 0.00274 ( 5) SS BOND : angle 0.82463 ( 10) hydrogen bonds : bond 0.03732 ( 444) hydrogen bonds : angle 4.68765 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.371 Fit side-chains REVERT: R 38 ILE cc_start: 0.8663 (tp) cc_final: 0.8437 (tp) REVERT: R 114 PHE cc_start: 0.8388 (t80) cc_final: 0.8160 (t80) REVERT: R 282 ILE cc_start: 0.8232 (tt) cc_final: 0.7876 (tp) REVERT: B 25 CYS cc_start: 0.8111 (m) cc_final: 0.7743 (m) REVERT: B 212 ASP cc_start: 0.8073 (t0) cc_final: 0.7609 (t0) REVERT: B 217 MET cc_start: 0.7731 (ppp) cc_final: 0.7246 (ppp) REVERT: B 219 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7666 (ttm170) REVERT: B 251 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8181 (mtt-85) REVERT: B 258 ASP cc_start: 0.7595 (t70) cc_final: 0.7129 (t0) REVERT: B 304 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8252 (mtm180) REVERT: A 23 LYS cc_start: 0.8059 (tttp) cc_final: 0.7811 (tttp) REVERT: A 80 ASN cc_start: 0.8213 (m110) cc_final: 0.7865 (m110) REVERT: A 148 LEU cc_start: 0.8484 (mp) cc_final: 0.8199 (mt) REVERT: A 195 ASP cc_start: 0.8092 (m-30) cc_final: 0.7822 (m-30) REVERT: A 217 CYS cc_start: 0.7449 (m) cc_final: 0.7166 (m) REVERT: A 232 ARG cc_start: 0.8222 (ttp80) cc_final: 0.8005 (ttp-110) outliers start: 18 outliers final: 16 residues processed: 200 average time/residue: 0.4971 time to fit residues: 106.5210 Evaluate side-chains 207 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114458 restraints weight = 11820.646| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.87 r_work: 0.3423 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8649 Z= 0.155 Angle : 0.518 9.377 11728 Z= 0.273 Chirality : 0.043 0.182 1318 Planarity : 0.004 0.041 1493 Dihedral : 4.166 44.919 1172 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.18 % Allowed : 17.41 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.11 (0.27), residues: 1059 helix: 2.14 (0.26), residues: 414 sheet: -0.14 (0.33), residues: 229 loop : -0.11 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.016 0.001 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.015 0.002 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8644) covalent geometry : angle 0.51740 (11718) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.86284 ( 10) hydrogen bonds : bond 0.03805 ( 444) hydrogen bonds : angle 4.71165 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.241 Fit side-chains REVERT: R 38 ILE cc_start: 0.8653 (tp) cc_final: 0.8423 (tp) REVERT: R 282 ILE cc_start: 0.8224 (tt) cc_final: 0.7870 (tp) REVERT: B 25 CYS cc_start: 0.8101 (m) cc_final: 0.7735 (m) REVERT: B 212 ASP cc_start: 0.8059 (t0) cc_final: 0.7594 (t0) REVERT: B 217 MET cc_start: 0.7717 (ppp) cc_final: 0.7217 (ppp) REVERT: B 219 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7647 (ttm170) REVERT: B 251 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (mtt-85) REVERT: B 258 ASP cc_start: 0.7596 (t70) cc_final: 0.7105 (t0) REVERT: B 304 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8263 (mtm180) REVERT: A 23 LYS cc_start: 0.8071 (tttp) cc_final: 0.7824 (tttp) REVERT: A 148 LEU cc_start: 0.8500 (mp) cc_final: 0.8231 (mt) REVERT: A 195 ASP cc_start: 0.8096 (m-30) cc_final: 0.7814 (m-30) REVERT: A 217 CYS cc_start: 0.7560 (m) cc_final: 0.7268 (m) REVERT: A 232 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7988 (ttp-110) outliers start: 20 outliers final: 15 residues processed: 197 average time/residue: 0.5017 time to fit residues: 105.6784 Evaluate side-chains 204 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 3 GLN A 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113607 restraints weight = 11871.636| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.87 r_work: 0.3405 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8649 Z= 0.212 Angle : 0.562 9.439 11728 Z= 0.293 Chirality : 0.046 0.350 1318 Planarity : 0.004 0.042 1493 Dihedral : 4.313 46.489 1172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.96 % Allowed : 17.52 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1059 helix: 1.92 (0.25), residues: 420 sheet: -0.02 (0.33), residues: 216 loop : -0.30 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.016 0.002 TYR R 180 PHE 0.018 0.001 PHE R 13 TRP 0.016 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8644) covalent geometry : angle 0.56191 (11718) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.03196 ( 10) hydrogen bonds : bond 0.04112 ( 444) hydrogen bonds : angle 4.80858 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.96 seconds wall clock time: 55 minutes 51.55 seconds (3351.55 seconds total)