Starting phenix.real_space_refine on Sun May 11 02:48:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8s_39057/05_2025/8y8s_39057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8s_39057/05_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_39057/05_2025/8y8s_39057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8s_39057/05_2025/8y8s_39057.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8s_39057/05_2025/8y8s_39057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8s_39057/05_2025/8y8s_39057.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.42, per 1000 atoms: 0.72 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.76 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: 2.05 Time building geometry restraints manager: 2.40 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.010 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.220 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- 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 : 4.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (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 TRP 0.004 0.001 TRP C 243 HIS 0.001 0.000 HIS D 268 PHE 0.007 0.001 PHE C 113 TYR 0.013 0.001 TYR D 124 ARG 0.007 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.27967 ( 492) hydrogen bonds : angle 7.61865 ( 1458) covalent geometry : bond 0.00176 ( 7793) covalent geometry : angle 0.41819 (10661) *********************** 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 : 0.802 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: 0.1623 time to fit residues: 24.5937 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 : 0.794 ------------------------------------------------------------------------------- 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 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.129841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107800 restraints weight = 8611.088| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.55 r_work: 0.2950 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7793 Z= 0.143 Angle : 0.535 6.967 10661 Z= 0.284 Chirality : 0.039 0.147 1229 Planarity : 0.004 0.040 1344 Dihedral : 5.838 47.261 1097 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1003 helix: 1.34 (0.19), residues: 675 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.001 0.000 HIS D 268 PHE 0.012 0.001 PHE C 113 TYR 0.018 0.001 TYR B 124 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.06049 ( 492) hydrogen bonds : angle 4.18373 ( 1458) covalent geometry : bond 0.00320 ( 7793) covalent geometry : angle 0.53499 (10661) *********************** 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 117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.812 Fit side-chains REVERT: B 92 PHE cc_start: 0.8591 (t80) cc_final: 0.8244 (t80) REVERT: B 212 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 219 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7860 (t0) REVERT: C 263 LEU cc_start: 0.8231 (mt) cc_final: 0.8027 (mt) REVERT: D 155 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6601 (mp) REVERT: D 157 MET cc_start: 0.7780 (mmm) cc_final: 0.7199 (mpp) outliers start: 35 outliers final: 22 residues processed: 112 average time/residue: 0.1283 time to fit residues: 22.3015 Evaluate side-chains 105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 186 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 36 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 191 GLU 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 110 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.104289 restraints weight = 8720.487| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.60 r_work: 0.2919 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7793 Z= 0.139 Angle : 0.509 7.600 10661 Z= 0.264 Chirality : 0.039 0.141 1229 Planarity : 0.004 0.042 1344 Dihedral : 4.576 36.486 1073 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.15 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1003 helix: 1.63 (0.19), residues: 683 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 53 PHE 0.023 0.001 PHE C 162 TYR 0.018 0.001 TYR B 124 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.05577 ( 492) hydrogen bonds : angle 3.99463 ( 1458) covalent geometry : bond 0.00324 ( 7793) covalent geometry : angle 0.50899 (10661) *********************** 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 115 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.810 Fit side-chains REVERT: B 92 PHE cc_start: 0.8607 (t80) cc_final: 0.8236 (t80) REVERT: C 263 LEU cc_start: 0.8238 (mt) cc_final: 0.8032 (mt) REVERT: D 157 MET cc_start: 0.7719 (mmm) cc_final: 0.7138 (mpp) outliers start: 32 outliers final: 29 residues processed: 109 average time/residue: 0.1328 time to fit residues: 22.3117 Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 219 ASP 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 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 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 99 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 155 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 C 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.132370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109317 restraints weight = 8600.978| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.63 r_work: 0.2978 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7793 Z= 0.102 Angle : 0.466 6.823 10661 Z= 0.242 Chirality : 0.037 0.133 1229 Planarity : 0.004 0.040 1344 Dihedral : 4.442 37.842 1073 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.98 % Allowed : 20.10 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1003 helix: 2.00 (0.19), residues: 681 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.001 0.000 HIS A 81 PHE 0.019 0.001 PHE C 162 TYR 0.017 0.001 TYR B 124 ARG 0.003 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 492) hydrogen bonds : angle 3.82084 ( 1458) covalent geometry : bond 0.00210 ( 7793) covalent geometry : angle 0.46585 (10661) *********************** 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 102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.868 Fit side-chains REVERT: B 92 PHE cc_start: 0.8655 (t80) cc_final: 0.8288 (t80) REVERT: B 219 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7838 (t0) REVERT: D 157 MET cc_start: 0.7660 (mmm) cc_final: 0.7142 (mpp) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 0.1308 time to fit residues: 20.0679 Evaluate side-chains 93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 42 SER Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain C residue 19 TYR 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 D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.132923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.108998 restraints weight = 8560.448| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.58 r_work: 0.2983 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1887 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= 0.100 Angle : 0.464 8.081 10661 Z= 0.237 Chirality : 0.037 0.131 1229 Planarity : 0.004 0.041 1344 Dihedral : 4.311 38.334 1072 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.76 % Allowed : 19.33 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1003 helix: 2.18 (0.19), residues: 679 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 128 HIS 0.001 0.000 HIS B 81 PHE 0.017 0.001 PHE C 162 TYR 0.018 0.001 TYR B 124 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 492) hydrogen bonds : angle 3.73610 ( 1458) covalent geometry : bond 0.00207 ( 7793) covalent geometry : angle 0.46433 (10661) *********************** 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 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.829 Fit side-chains REVERT: B 92 PHE cc_start: 0.8640 (t80) cc_final: 0.8258 (t80) REVERT: C 264 MET cc_start: 0.8298 (mmm) cc_final: 0.7746 (mmt) REVERT: D 157 MET cc_start: 0.7524 (mmm) cc_final: 0.6977 (mpp) REVERT: D 193 PHE cc_start: 0.7882 (m-80) cc_final: 0.7606 (m-80) outliers start: 29 outliers final: 25 residues processed: 105 average time/residue: 0.1353 time to fit residues: 21.8236 Evaluate side-chains 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 171 LEU 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 42 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ASP 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 36 VAL 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 43 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.130031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.105853 restraints weight = 8581.223| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.58 r_work: 0.2945 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.003 0.028 7793 Z= 0.129 Angle : 0.494 8.322 10661 Z= 0.253 Chirality : 0.039 0.141 1229 Planarity : 0.004 0.042 1344 Dihedral : 4.430 42.023 1072 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1003 helix: 1.98 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 128 HIS 0.001 0.000 HIS A 53 PHE 0.025 0.001 PHE C 162 TYR 0.019 0.001 TYR B 124 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 492) hydrogen bonds : angle 3.77758 ( 1458) covalent geometry : bond 0.00301 ( 7793) covalent geometry : angle 0.49402 (10661) *********************** 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 117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.758 Fit side-chains REVERT: B 92 PHE cc_start: 0.8671 (t80) cc_final: 0.8291 (t80) REVERT: B 158 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7984 (m) REVERT: C 264 MET cc_start: 0.8351 (mmm) cc_final: 0.7890 (mmt) REVERT: D 157 MET cc_start: 0.7632 (mmm) cc_final: 0.6998 (mpp) outliers start: 34 outliers final: 29 residues processed: 109 average time/residue: 0.1241 time to fit residues: 20.9105 Evaluate side-chains 112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 A residue 219 ASP 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 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 251 LEU Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 19 TYR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107148 restraints weight = 8538.541| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.56 r_work: 0.2959 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1859 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= 0.113 Angle : 0.477 7.646 10661 Z= 0.245 Chirality : 0.038 0.138 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.433 45.017 1072 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.15 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1003 helix: 2.04 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 128 HIS 0.001 0.000 HIS A 53 PHE 0.022 0.001 PHE C 162 TYR 0.019 0.001 TYR B 124 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 492) hydrogen bonds : angle 3.74245 ( 1458) covalent geometry : bond 0.00253 ( 7793) covalent geometry : angle 0.47675 (10661) *********************** 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 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.835 Fit side-chains REVERT: B 92 PHE cc_start: 0.8652 (t80) cc_final: 0.8263 (t80) REVERT: C 264 MET cc_start: 0.8311 (mmm) cc_final: 0.7803 (mmt) REVERT: D 157 MET cc_start: 0.7658 (mmm) cc_final: 0.7115 (mpp) outliers start: 32 outliers final: 29 residues processed: 106 average time/residue: 0.1312 time to fit residues: 21.5621 Evaluate side-chains 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 A residue 219 ASP 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 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU 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 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 106 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 0.0050 chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.132024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107760 restraints weight = 8671.089| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.59 r_work: 0.2969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1930 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= 0.103 Angle : 0.465 7.494 10661 Z= 0.238 Chirality : 0.037 0.135 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.403 48.942 1072 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.02 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1003 helix: 2.11 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 128 HIS 0.001 0.000 HIS D 81 PHE 0.021 0.001 PHE C 162 TYR 0.020 0.001 TYR B 124 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 492) hydrogen bonds : angle 3.69365 ( 1458) covalent geometry : bond 0.00222 ( 7793) covalent geometry : angle 0.46508 (10661) *********************** 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 113 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.873 Fit side-chains REVERT: B 92 PHE cc_start: 0.8652 (t80) cc_final: 0.8259 (t80) REVERT: B 219 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7799 (t0) REVERT: C 264 MET cc_start: 0.8297 (mmm) cc_final: 0.7734 (mmt) REVERT: D 157 MET cc_start: 0.7602 (mmm) cc_final: 0.7078 (mpp) outliers start: 31 outliers final: 27 residues processed: 108 average time/residue: 0.1290 time to fit residues: 21.3972 Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 A residue 219 ASP 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 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 35 LEU 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 137 VAL Chi-restraints excluded: chain C residue 155 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.130176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.105832 restraints weight = 8648.114| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.59 r_work: 0.2946 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1874 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= 0.124 Angle : 0.487 7.954 10661 Z= 0.250 Chirality : 0.038 0.140 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.525 55.167 1072 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.02 % Allowed : 18.55 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 1003 helix: 1.99 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 128 HIS 0.001 0.000 HIS A 53 PHE 0.013 0.001 PHE B 225 TYR 0.019 0.001 TYR B 124 ARG 0.001 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 492) hydrogen bonds : angle 3.75267 ( 1458) covalent geometry : bond 0.00289 ( 7793) covalent geometry : angle 0.48713 (10661) *********************** 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 113 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.782 Fit side-chains REVERT: B 92 PHE cc_start: 0.8648 (t80) cc_final: 0.8261 (t80) REVERT: C 264 MET cc_start: 0.8314 (mmm) cc_final: 0.7807 (mmt) REVERT: D 157 MET cc_start: 0.7696 (mmm) cc_final: 0.7129 (mpp) outliers start: 31 outliers final: 29 residues processed: 108 average time/residue: 0.1256 time to fit residues: 21.0074 Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 A residue 219 ASP 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 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 267 CYS 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 155 LEU 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 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.132238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107987 restraints weight = 8620.255| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.58 r_work: 0.2975 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1972 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= 0.101 Angle : 0.463 7.431 10661 Z= 0.238 Chirality : 0.037 0.135 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.467 57.201 1072 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.89 % Allowed : 18.55 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1003 helix: 2.11 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 128 HIS 0.001 0.000 HIS D 81 PHE 0.014 0.001 PHE C 162 TYR 0.020 0.001 TYR B 124 ARG 0.001 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 492) hydrogen bonds : angle 3.68245 ( 1458) covalent geometry : bond 0.00213 ( 7793) covalent geometry : angle 0.46292 (10661) ********************** 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 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.835 Fit side-chains REVERT: B 92 PHE cc_start: 0.8655 (t80) cc_final: 0.8255 (t80) REVERT: B 219 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7801 (t0) REVERT: C 264 MET cc_start: 0.8281 (mmm) cc_final: 0.7691 (mmt) outliers start: 30 outliers final: 29 residues processed: 104 average time/residue: 0.1325 time to fit residues: 21.3285 Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 A residue 219 ASP 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 143 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 267 CYS 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 155 LEU 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 92 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.128134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.103825 restraints weight = 8573.344| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.58 r_work: 0.2916 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7793 Z= 0.167 Angle : 0.525 8.538 10661 Z= 0.270 Chirality : 0.040 0.148 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.542 48.727 1072 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.28 % Allowed : 18.42 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1003 helix: 1.85 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 128 HIS 0.002 0.000 HIS A 53 PHE 0.015 0.001 PHE B 225 TYR 0.020 0.001 TYR B 124 ARG 0.002 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 492) hydrogen bonds : angle 3.81677 ( 1458) covalent geometry : bond 0.00410 ( 7793) covalent geometry : angle 0.52462 (10661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.03 seconds wall clock time: 61 minutes 0.71 seconds (3660.71 seconds total)