Starting phenix.real_space_refine on Wed Sep 17 08:50:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8s_39057/09_2025/8y8s_39057.cif" } resolution = 3.03 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= 0.001 sd= 0.074 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 40 5.16 5 C 5011 2.51 5 N 1228 2.21 5 O 1298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7577 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1925 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain: "B" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1876 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "C" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1888 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 12, 'TRANS': 239} Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1888 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 12, 'TRANS': 239} Time building chain proxies: 2.18, per 1000 atoms: 0.29 Number of scatterers: 7577 At special positions: 0 Unit cell: (71.355, 83.415, 82.41, 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 40 16.00 O 1298 8.00 N 1228 7.00 C 5011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.15 Conformation dependent library (CDL) restraints added in 482.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.663A pdb=" N ALA A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 4.015A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 99 through 123 removed outlier: 3.846A pdb=" N ILE A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 removed outlier: 4.551A pdb=" N ALA A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.707A pdb=" N ILE A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 156 through 180 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 215 through 229 Proline residue: A 222 - end of helix removed outlier: 3.660A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.811A pdb=" N VAL A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 265 Proline residue: A 250 - end of helix removed outlier: 3.533A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 49 removed outlier: 3.617A pdb=" N SER B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 3.786A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLN B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 99 through 123 removed outlier: 3.647A pdb=" N ILE B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 143 through 147 removed outlier: 3.609A pdb=" N ILE B 146 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 147' Processing helix chain 'B' and resid 156 through 179 removed outlier: 3.986A pdb=" N PHE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.633A pdb=" N VAL B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 230 Proline residue: B 222 - end of helix removed outlier: 3.683A pdb=" N GLY B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.924A pdb=" N VAL B 235 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Proline residue: B 250 - end of helix removed outlier: 3.738A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 49 removed outlier: 3.656A pdb=" N SER C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 79 removed outlier: 3.600A pdb=" N THR C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLN C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 77 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 99 through 123 removed outlier: 4.052A pdb=" N ILE C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.548A pdb=" N PHE C 147 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 180 removed outlier: 3.810A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 178 " --> pdb=" O CYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 206 removed outlier: 3.896A pdb=" N PHE C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 230 Proline residue: C 222 - end of helix removed outlier: 3.725A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.126A pdb=" N VAL C 235 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 265 Proline residue: C 250 - end of helix removed outlier: 3.658A pdb=" N ILE C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'D' and resid 20 through 49 removed outlier: 3.772A pdb=" N SER D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.816A pdb=" N ILE D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 99 through 123 removed outlier: 3.774A pdb=" N ILE D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 112 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.610A pdb=" N PHE D 147 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 179 removed outlier: 4.019A pdb=" N PHE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 178 " --> pdb=" O CYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 215 through 230 Proline residue: D 222 - end of helix removed outlier: 3.770A pdb=" N LEU D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.734A pdb=" N THR D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 265 Proline residue: D 250 - end of helix removed outlier: 3.669A pdb=" N ILE D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 removed outlier: 3.982A pdb=" N LEU D 269 " --> pdb=" O GLY D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' 492 hydrogen bonds defined for protein. 1458 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: 1.12 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2362 1.34 - 1.46: 1750 1.46 - 1.58: 3621 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7793 Sorted by residual: bond pdb=" C VAL A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.03e-01 bond pdb=" CG1 ILE B 178 " pdb=" CD1 ILE B 178 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.07e-01 bond pdb=" CG PRO C 246 " pdb=" CD PRO C 246 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.25e-01 bond pdb=" CA VAL D 214 " pdb=" C VAL D 214 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.27e-02 6.20e+03 3.67e-01 bond pdb=" C SER C 249 " pdb=" N PRO C 250 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.47e-01 ... (remaining 7788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 10453 1.13 - 2.25: 138 2.25 - 3.38: 49 3.38 - 4.51: 11 4.51 - 5.63: 10 Bond angle restraints: 10661 Sorted by residual: angle pdb=" C ILE A 17 " pdb=" N ARG A 18 " pdb=" CA ARG A 18 " ideal model delta sigma weight residual 122.61 125.46 -2.85 1.56e+00 4.11e-01 3.34e+00 angle pdb=" N GLY D 111 " pdb=" CA GLY D 111 " pdb=" C GLY D 111 " ideal model delta sigma weight residual 113.18 108.99 4.19 2.37e+00 1.78e-01 3.13e+00 angle pdb=" N GLY A 111 " pdb=" CA GLY A 111 " pdb=" C GLY A 111 " ideal model delta sigma weight residual 113.18 109.12 4.06 2.37e+00 1.78e-01 2.94e+00 angle pdb=" N GLY B 111 " pdb=" CA GLY B 111 " pdb=" C GLY B 111 " ideal model delta sigma weight residual 113.18 109.17 4.01 2.37e+00 1.78e-01 2.87e+00 angle pdb=" C VAL C 179 " pdb=" N ASP C 180 " pdb=" CA ASP C 180 " ideal model delta sigma weight residual 121.80 125.92 -4.12 2.44e+00 1.68e-01 2.86e+00 ... (remaining 10656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 3733 16.71 - 33.43: 418 33.43 - 50.14: 145 50.14 - 66.85: 23 66.85 - 83.57: 10 Dihedral angle restraints: 4329 sinusoidal: 1533 harmonic: 2796 Sorted by residual: dihedral pdb=" CA GLY C 111 " pdb=" C GLY C 111 " pdb=" N ALA C 112 " pdb=" CA ALA C 112 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY B 111 " pdb=" C GLY B 111 " pdb=" N ALA B 112 " pdb=" CA ALA B 112 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLY D 111 " pdb=" C GLY D 111 " pdb=" N ALA D 112 " pdb=" CA ALA D 112 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 4326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 755 0.027 - 0.054: 330 0.054 - 0.082: 99 0.082 - 0.109: 40 0.109 - 0.136: 5 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CA SER C 249 " pdb=" N SER C 249 " pdb=" C SER C 249 " pdb=" CB SER C 249 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA SER A 249 " pdb=" N SER A 249 " pdb=" C SER A 249 " pdb=" CB SER A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA SER D 249 " pdb=" N SER D 249 " pdb=" C SER D 249 " pdb=" CB SER D 249 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1226 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 221 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO D 222 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 222 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 222 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 221 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 222 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 221 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 222 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.020 5.00e-02 4.00e+02 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2028 2.79 - 3.32: 6856 3.32 - 3.85: 12203 3.85 - 4.37: 14853 4.37 - 4.90: 26221 Nonbonded interactions: 62161 Sorted by model distance: nonbonded pdb=" O GLN B 164 " pdb=" OG1 THR B 168 " model vdw 2.265 3.040 nonbonded pdb=" O VAL D 245 " pdb=" OG SER D 249 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP B 180 " pdb=" OH TYR B 261 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 123 " pdb=" O SER B 205 " model vdw 2.303 3.040 nonbonded pdb=" O PHE A 56 " pdb=" ND2 ASN A 60 " model vdw 2.305 3.120 ... (remaining 62156 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 270) selection = chain 'B' selection = (chain 'C' and resid 20 through 270) selection = (chain 'D' and resid 20 through 270) } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.030 Process input model: 9.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.002 0.028 7793 Z= 0.079 Angle : 0.418 5.633 10661 Z= 0.211 Chirality : 0.035 0.136 1229 Planarity : 0.004 0.038 1344 Dihedral : 16.234 83.568 2571 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.85 % Allowed : 22.57 % Favored : 74.58 % 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 aren not related in a simple way. whole: -0.75 (0.25), residues: 1003 helix: -0.01 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.013 0.001 TYR D 124 PHE 0.007 0.001 PHE C 113 TRP 0.004 0.001 TRP C 243 HIS 0.001 0.000 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 7793) covalent geometry : angle 0.41819 (10661) hydrogen bonds : bond 0.27967 ( 492) hydrogen bonds : angle 7.61865 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.279 Fit side-chains REVERT: B 92 PHE cc_start: 0.8683 (t80) cc_final: 0.8385 (t80) REVERT: D 60 ASN cc_start: 0.8878 (m-40) cc_final: 0.8653 (m110) REVERT: D 157 MET cc_start: 0.7651 (mmm) cc_final: 0.7091 (mpp) outliers start: 22 outliers final: 21 residues processed: 106 average time/residue: 0.0789 time to fit residues: 12.0491 Evaluate side-chains 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 212 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.106722 restraints weight = 8743.527| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.58 r_work: 0.2948 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7793 Z= 0.130 Angle : 0.508 6.107 10661 Z= 0.273 Chirality : 0.038 0.141 1229 Planarity : 0.004 0.038 1344 Dihedral : 5.615 47.445 1097 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.24 % Allowed : 20.23 % Favored : 76.52 % 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 aren not related in a simple way. whole: 0.88 (0.27), residues: 1003 helix: 1.54 (0.19), residues: 675 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.017 0.001 TYR B 124 PHE 0.012 0.001 PHE B 113 TRP 0.007 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7793) covalent geometry : angle 0.50772 (10661) hydrogen bonds : bond 0.06192 ( 492) hydrogen bonds : angle 4.26315 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.277 Fit side-chains REVERT: B 92 PHE cc_start: 0.8566 (t80) cc_final: 0.8238 (t80) REVERT: B 212 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8593 (t80) REVERT: B 219 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7863 (t0) REVERT: D 155 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6420 (mp) REVERT: D 157 MET cc_start: 0.7731 (mmm) cc_final: 0.7134 (mpp) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 0.0598 time to fit residues: 9.8956 Evaluate side-chains 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 155 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.102780 restraints weight = 8666.529| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.57 r_work: 0.2893 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7793 Z= 0.184 Angle : 0.555 8.628 10661 Z= 0.287 Chirality : 0.041 0.149 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.652 37.954 1072 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.80 % Allowed : 18.81 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1003 helix: 1.49 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.019 0.001 TYR B 124 PHE 0.018 0.002 PHE B 225 TRP 0.008 0.001 TRP A 128 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7793) covalent geometry : angle 0.55496 (10661) hydrogen bonds : bond 0.06359 ( 492) hydrogen bonds : angle 4.08622 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.272 Fit side-chains REVERT: A 234 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: B 92 PHE cc_start: 0.8611 (t80) cc_final: 0.8232 (t80) REVERT: D 155 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6693 (mp) REVERT: D 157 MET cc_start: 0.7785 (mmm) cc_final: 0.7173 (mpp) outliers start: 37 outliers final: 29 residues processed: 112 average time/residue: 0.0551 time to fit residues: 9.7238 Evaluate side-chains 113 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.130275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.106007 restraints weight = 8696.222| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.59 r_work: 0.2942 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7793 Z= 0.115 Angle : 0.486 7.256 10661 Z= 0.252 Chirality : 0.037 0.138 1229 Planarity : 0.004 0.041 1344 Dihedral : 4.532 41.220 1072 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.11 % Allowed : 19.71 % Favored : 77.17 % 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 aren not related in a simple way. whole: 1.25 (0.27), residues: 1003 helix: 1.83 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.018 0.001 TYR B 124 PHE 0.010 0.001 PHE B 225 TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7793) covalent geometry : angle 0.48622 (10661) hydrogen bonds : bond 0.04675 ( 492) hydrogen bonds : angle 3.88491 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.278 Fit side-chains REVERT: B 45 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: B 92 PHE cc_start: 0.8601 (t80) cc_final: 0.8221 (t80) REVERT: D 157 MET cc_start: 0.7704 (mmm) cc_final: 0.7129 (mpp) outliers start: 24 outliers final: 20 residues processed: 106 average time/residue: 0.0562 time to fit residues: 9.4142 Evaluate side-chains 102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 56 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: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108797 restraints weight = 8632.651| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.57 r_work: 0.2980 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7793 Z= 0.102 Angle : 0.465 6.815 10661 Z= 0.240 Chirality : 0.037 0.132 1229 Planarity : 0.004 0.041 1344 Dihedral : 4.410 43.259 1072 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.02 % Allowed : 19.20 % Favored : 76.78 % 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 aren not related in a simple way. whole: 1.55 (0.27), residues: 1003 helix: 2.10 (0.19), residues: 679 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.018 0.001 TYR B 124 PHE 0.010 0.001 PHE B 225 TRP 0.005 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7793) covalent geometry : angle 0.46473 (10661) hydrogen bonds : bond 0.04021 ( 492) hydrogen bonds : angle 3.77605 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.275 Fit side-chains REVERT: A 45 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: B 45 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: B 92 PHE cc_start: 0.8661 (t80) cc_final: 0.8283 (t80) REVERT: B 219 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7745 (t0) REVERT: C 264 MET cc_start: 0.8305 (mmm) cc_final: 0.7778 (mmt) REVERT: D 157 MET cc_start: 0.7617 (mmm) cc_final: 0.7093 (mpp) outliers start: 31 outliers final: 25 residues processed: 103 average time/residue: 0.0580 time to fit residues: 9.3152 Evaluate side-chains 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.103446 restraints weight = 8721.488| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.59 r_work: 0.2903 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7793 Z= 0.180 Angle : 0.540 8.710 10661 Z= 0.277 Chirality : 0.041 0.150 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.673 50.171 1072 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.54 % Allowed : 18.94 % Favored : 76.52 % 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 aren not related in a simple way. whole: 1.14 (0.27), residues: 1003 helix: 1.73 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.020 0.001 TYR B 124 PHE 0.017 0.001 PHE B 225 TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7793) covalent geometry : angle 0.53980 (10661) hydrogen bonds : bond 0.05623 ( 492) hydrogen bonds : angle 3.90551 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.248 Fit side-chains REVERT: B 92 PHE cc_start: 0.8686 (t80) cc_final: 0.8305 (t80) REVERT: B 212 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8643 (t80) REVERT: D 157 MET cc_start: 0.7764 (mmm) cc_final: 0.7181 (mpp) outliers start: 35 outliers final: 29 residues processed: 109 average time/residue: 0.0540 time to fit residues: 9.2584 Evaluate side-chains 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.103756 restraints weight = 8633.921| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.58 r_work: 0.2915 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7793 Z= 0.157 Angle : 0.520 8.257 10661 Z= 0.268 Chirality : 0.040 0.147 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.782 58.469 1072 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.54 % Allowed : 18.94 % Favored : 76.52 % 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 aren not related in a simple way. whole: 1.10 (0.27), residues: 1003 helix: 1.71 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.020 0.001 TYR B 124 PHE 0.014 0.001 PHE B 225 TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7793) covalent geometry : angle 0.52021 (10661) hydrogen bonds : bond 0.05286 ( 492) hydrogen bonds : angle 3.86938 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.286 Fit side-chains REVERT: B 92 PHE cc_start: 0.8627 (t80) cc_final: 0.8238 (t80) REVERT: D 157 MET cc_start: 0.7715 (mmm) cc_final: 0.7181 (mpp) outliers start: 35 outliers final: 34 residues processed: 106 average time/residue: 0.0571 time to fit residues: 9.3776 Evaluate side-chains 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.107547 restraints weight = 8626.711| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.64 r_work: 0.2961 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7793 Z= 0.108 Angle : 0.472 7.292 10661 Z= 0.243 Chirality : 0.037 0.137 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.541 52.196 1072 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.41 % Allowed : 19.07 % Favored : 76.52 % 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 aren not related in a simple way. whole: 1.41 (0.27), residues: 1003 helix: 1.96 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.019 0.001 TYR B 124 PHE 0.009 0.001 PHE B 225 TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7793) covalent geometry : angle 0.47216 (10661) hydrogen bonds : bond 0.04213 ( 492) hydrogen bonds : angle 3.75437 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.281 Fit side-chains REVERT: B 92 PHE cc_start: 0.8587 (t80) cc_final: 0.8192 (t80) REVERT: C 264 MET cc_start: 0.8365 (mmm) cc_final: 0.7919 (mmt) REVERT: D 157 MET cc_start: 0.7736 (mmm) cc_final: 0.7177 (mpp) outliers start: 34 outliers final: 26 residues processed: 107 average time/residue: 0.0522 time to fit residues: 8.6898 Evaluate side-chains 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103692 restraints weight = 8639.750| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.59 r_work: 0.2914 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7793 Z= 0.155 Angle : 0.520 8.370 10661 Z= 0.267 Chirality : 0.040 0.146 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.546 44.535 1072 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.76 % Allowed : 19.46 % Favored : 76.78 % 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 aren not related in a simple way. whole: 1.21 (0.27), residues: 1003 helix: 1.79 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.020 0.001 TYR B 124 PHE 0.015 0.001 PHE B 225 TRP 0.006 0.001 TRP C 231 HIS 0.002 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7793) covalent geometry : angle 0.51992 (10661) hydrogen bonds : bond 0.05143 ( 492) hydrogen bonds : angle 3.83414 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.174 Fit side-chains REVERT: B 92 PHE cc_start: 0.8671 (t80) cc_final: 0.8275 (t80) REVERT: D 157 MET cc_start: 0.7641 (mmm) cc_final: 0.7073 (mpp) outliers start: 29 outliers final: 28 residues processed: 102 average time/residue: 0.0549 time to fit residues: 8.8273 Evaluate side-chains 104 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104761 restraints weight = 8577.341| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.58 r_work: 0.2927 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7793 Z= 0.134 Angle : 0.499 7.871 10661 Z= 0.257 Chirality : 0.039 0.143 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.469 38.061 1072 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.76 % Allowed : 19.20 % Favored : 77.04 % 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 aren not related in a simple way. whole: 1.24 (0.27), residues: 1003 helix: 1.81 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.020 0.001 TYR B 124 PHE 0.012 0.001 PHE B 225 TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7793) covalent geometry : angle 0.49910 (10661) hydrogen bonds : bond 0.04817 ( 492) hydrogen bonds : angle 3.80294 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.286 Fit side-chains REVERT: B 92 PHE cc_start: 0.8668 (t80) cc_final: 0.8271 (t80) REVERT: C 264 MET cc_start: 0.8414 (mmm) cc_final: 0.7959 (mmt) REVERT: D 157 MET cc_start: 0.7673 (mmm) cc_final: 0.7109 (mpp) outliers start: 29 outliers final: 29 residues processed: 101 average time/residue: 0.0591 time to fit residues: 9.4308 Evaluate side-chains 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106809 restraints weight = 8536.100| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.58 r_work: 0.2959 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7793 Z= 0.108 Angle : 0.471 7.324 10661 Z= 0.243 Chirality : 0.037 0.137 1229 Planarity : 0.004 0.044 1344 Dihedral : 4.306 34.546 1072 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.50 % Allowed : 19.46 % Favored : 77.04 % 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 aren not related in a simple way. whole: 1.42 (0.27), residues: 1003 helix: 1.97 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.019 0.001 TYR B 124 PHE 0.010 0.001 PHE B 225 TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7793) covalent geometry : angle 0.47074 (10661) hydrogen bonds : bond 0.04144 ( 492) hydrogen bonds : angle 3.72590 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.41 seconds wall clock time: 30 minutes 18.71 seconds (1818.71 seconds total)