Starting phenix.real_space_refine on Fri Jul 25 08:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8s_39057/07_2025/8y8s_39057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8s_39057/07_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_39057/07_2025/8y8s_39057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8s_39057/07_2025/8y8s_39057.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8s_39057/07_2025/8y8s_39057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8s_39057/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.16, per 1000 atoms: 0.68 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: 1.58 Conformation dependent library (CDL) restraints added in 977.2 milliseconds 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: 0.64 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: 1.98 Time building geometry restraints manager: 1.93 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.800 Find NCS groups from input model: 0.350 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- 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 : 0.792 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: 0.1664 time to fit residues: 25.2126 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 : 0.923 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107779 restraints weight = 8611.083| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.56 r_work: 0.2951 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- 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 : 0.802 Fit side-chains REVERT: B 92 PHE cc_start: 0.8593 (t80) cc_final: 0.8247 (t80) REVERT: B 212 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 219 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7866 (t0) REVERT: C 263 LEU cc_start: 0.8229 (mt) cc_final: 0.8025 (mt) REVERT: D 155 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6601 (mp) REVERT: D 157 MET cc_start: 0.7783 (mmm) cc_final: 0.7198 (mpp) outliers start: 35 outliers final: 22 residues processed: 112 average time/residue: 0.1315 time to fit residues: 22.7258 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 : 0.797 ------------------------------------------------------------------------------- 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: 0.0570 chunk 17 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 = 0.132175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107987 restraints weight = 8707.243| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.60 r_work: 0.2974 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1681 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= 0.103 Angle : 0.467 6.603 10661 Z= 0.242 Chirality : 0.037 0.133 1229 Planarity : 0.004 0.039 1344 Dihedral : 4.360 36.230 1073 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.37 % Allowed : 19.58 % 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: 1.35 (0.27), residues: 1003 helix: 1.96 (0.19), residues: 677 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 326 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 0.028 0.001 PHE C 162 TYR 0.017 0.001 TYR B 124 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 492) hydrogen bonds : angle 3.89893 ( 1458) covalent geometry : bond 0.00211 ( 7793) covalent geometry : angle 0.46725 (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 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.741 Fit side-chains REVERT: B 45 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: B 92 PHE cc_start: 0.8660 (t80) cc_final: 0.8304 (t80) REVERT: B 219 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7826 (t0) REVERT: D 157 MET cc_start: 0.7644 (mmm) cc_final: 0.7125 (mpp) outliers start: 26 outliers final: 18 residues processed: 107 average time/residue: 0.1293 time to fit residues: 21.3437 Evaluate side-chains 100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 45 GLN Chi-restraints excluded: chain B residue 125 ASP 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 137 VAL Chi-restraints excluded: chain C residue 155 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 94 optimal weight: 0.0670 chunk 36 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.133665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.110174 restraints weight = 8620.242| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.54 r_work: 0.3000 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1866 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= 0.097 Angle : 0.461 7.555 10661 Z= 0.237 Chirality : 0.037 0.131 1229 Planarity : 0.004 0.040 1344 Dihedral : 4.235 36.241 1072 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.46 % Allowed : 20.23 % 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: 1.58 (0.27), residues: 1003 helix: 2.18 (0.19), residues: 677 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 128 HIS 0.001 0.000 HIS A 81 PHE 0.018 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 0.03919 ( 492) hydrogen bonds : angle 3.76920 ( 1458) covalent geometry : bond 0.00195 ( 7793) covalent geometry : angle 0.46076 (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 99 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.730 Fit side-chains REVERT: B 92 PHE cc_start: 0.8654 (t80) cc_final: 0.8289 (t80) REVERT: C 264 MET cc_start: 0.8302 (mmm) cc_final: 0.7744 (mmt) REVERT: D 157 MET cc_start: 0.7501 (mmm) cc_final: 0.6991 (mpp) outliers start: 19 outliers final: 15 residues processed: 97 average time/residue: 0.1344 time to fit residues: 20.1154 Evaluate side-chains 95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 171 LEU 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 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 137 VAL Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 212 TYR 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: 0.0030 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.108159 restraints weight = 8581.049| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.58 r_work: 0.2974 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 0.023 7793 Z= 0.106 Angle : 0.468 7.655 10661 Z= 0.240 Chirality : 0.037 0.134 1229 Planarity : 0.004 0.041 1344 Dihedral : 4.241 35.218 1072 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.76 % Allowed : 18.55 % Favored : 77.69 % 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: 1.64 (0.27), residues: 1003 helix: 2.21 (0.19), residues: 679 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 128 HIS 0.001 0.000 HIS C 268 PHE 0.024 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 0.04156 ( 492) hydrogen bonds : angle 3.74201 ( 1458) covalent geometry : bond 0.00228 ( 7793) covalent geometry : angle 0.46836 (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 : 0.787 Fit side-chains REVERT: B 45 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: B 92 PHE cc_start: 0.8644 (t80) cc_final: 0.8263 (t80) REVERT: B 219 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 264 MET cc_start: 0.8311 (mmm) cc_final: 0.7793 (mmt) REVERT: D 157 MET cc_start: 0.7478 (mmm) cc_final: 0.6966 (mpp) outliers start: 29 outliers final: 23 residues processed: 104 average time/residue: 0.1484 time to fit residues: 24.2613 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 : 1.033 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 42 SER 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 219 ASP 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 137 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110219 restraints weight = 8549.947| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.47 r_work: 0.2995 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1903 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= 0.102 Angle : 0.462 7.581 10661 Z= 0.237 Chirality : 0.037 0.133 1229 Planarity : 0.004 0.042 1344 Dihedral : 4.216 34.701 1072 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.24 % Allowed : 19.20 % 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: 1.71 (0.27), residues: 1003 helix: 2.26 (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 0.004 0.001 TRP A 128 HIS 0.001 0.000 HIS A 53 PHE 0.021 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 0.03983 ( 492) hydrogen bonds : angle 3.69801 ( 1458) covalent geometry : bond 0.00220 ( 7793) covalent geometry : angle 0.46229 (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 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 1.725 Fit side-chains REVERT: A 45 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: B 45 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: B 92 PHE cc_start: 0.8647 (t80) cc_final: 0.8261 (t80) REVERT: B 219 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7691 (t0) REVERT: C 264 MET cc_start: 0.8261 (mmm) cc_final: 0.7705 (mmt) REVERT: D 157 MET cc_start: 0.7480 (mmm) cc_final: 0.6966 (mpp) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.1732 time to fit residues: 27.3365 Evaluate side-chains 103 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 45 GLN 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 B residue 35 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 251 LEU 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 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=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: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 41 optimal weight: 0.0020 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.132422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108418 restraints weight = 8521.061| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.57 r_work: 0.2981 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1936 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= 0.103 Angle : 0.464 7.615 10661 Z= 0.237 Chirality : 0.037 0.134 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.227 34.214 1072 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.50 % Allowed : 19.20 % 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: 1.66 (0.27), residues: 1003 helix: 2.20 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 128 HIS 0.001 0.000 HIS C 268 PHE 0.011 0.001 PHE B 225 TYR 0.019 0.001 TYR B 124 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 492) hydrogen bonds : angle 3.68922 ( 1458) covalent geometry : bond 0.00224 ( 7793) covalent geometry : angle 0.46377 (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 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.823 Fit side-chains REVERT: A 45 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: B 45 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: B 92 PHE cc_start: 0.8651 (t80) cc_final: 0.8260 (t80) REVERT: B 219 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 264 MET cc_start: 0.8270 (mmm) cc_final: 0.7711 (mmt) REVERT: D 157 MET cc_start: 0.7499 (mmm) cc_final: 0.6963 (mpp) outliers start: 27 outliers final: 24 residues processed: 104 average time/residue: 0.1569 time to fit residues: 25.4316 Evaluate side-chains 109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 45 GLN 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 42 SER Chi-restraints excluded: chain B residue 45 GLN 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 158 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0060 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.134347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.110275 restraints weight = 8671.432| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.59 r_work: 0.3007 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7793 Z= 0.092 Angle : 0.449 7.311 10661 Z= 0.229 Chirality : 0.036 0.130 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.148 34.225 1072 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.24 % Allowed : 19.33 % 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: 1.82 (0.27), residues: 1003 helix: 2.37 (0.19), residues: 679 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 128 HIS 0.001 0.000 HIS B 81 PHE 0.015 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 0.03556 ( 492) hydrogen bonds : angle 3.64203 ( 1458) covalent geometry : bond 0.00184 ( 7793) covalent geometry : angle 0.44941 (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 115 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.738 Fit side-chains REVERT: A 45 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: B 45 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: B 92 PHE cc_start: 0.8629 (t80) cc_final: 0.8237 (t80) REVERT: B 219 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7740 (t0) REVERT: C 264 MET cc_start: 0.8233 (mmm) cc_final: 0.7633 (mmt) REVERT: D 157 MET cc_start: 0.7473 (mmm) cc_final: 0.6957 (mpp) REVERT: D 193 PHE cc_start: 0.7921 (m-80) cc_final: 0.7589 (m-80) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.1271 time to fit residues: 21.3545 Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 45 GLN 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 42 SER Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 61 LEU 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 251 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.105767 restraints weight = 8671.913| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.59 r_work: 0.2940 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7793 Z= 0.139 Angle : 0.498 8.261 10661 Z= 0.255 Chirality : 0.039 0.142 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.313 35.749 1072 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.50 % Allowed : 19.58 % 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: 1.49 (0.27), residues: 1003 helix: 2.06 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 128 HIS 0.001 0.000 HIS C 81 PHE 0.019 0.001 PHE C 162 TYR 0.017 0.001 TYR B 124 ARG 0.002 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 492) hydrogen bonds : angle 3.73579 ( 1458) covalent geometry : bond 0.00333 ( 7793) covalent geometry : angle 0.49816 (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 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.726 Fit side-chains REVERT: A 45 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: B 92 PHE cc_start: 0.8651 (t80) cc_final: 0.8266 (t80) REVERT: B 158 VAL cc_start: 0.8158 (t) cc_final: 0.7958 (m) REVERT: B 219 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7768 (t0) REVERT: C 264 MET cc_start: 0.8311 (mmm) cc_final: 0.7807 (mmt) REVERT: D 157 MET cc_start: 0.7592 (mmm) cc_final: 0.6984 (mpp) outliers start: 27 outliers final: 20 residues processed: 104 average time/residue: 0.1290 time to fit residues: 20.7186 Evaluate side-chains 105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 45 GLN Chi-restraints excluded: chain A residue 143 THR 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 219 ASP Chi-restraints excluded: chain B residue 251 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 183 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108503 restraints weight = 8639.213| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.58 r_work: 0.2981 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2016 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= 0.099 Angle : 0.461 7.391 10661 Z= 0.236 Chirality : 0.037 0.133 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.258 36.221 1072 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.24 % Allowed : 19.33 % 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: 1.67 (0.27), residues: 1003 helix: 2.21 (0.19), residues: 685 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 318 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 0.020 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 0.03875 ( 492) hydrogen bonds : angle 3.66487 ( 1458) covalent geometry : bond 0.00207 ( 7793) covalent geometry : angle 0.46055 (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 109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.807 Fit side-chains REVERT: A 45 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: B 92 PHE cc_start: 0.8637 (t80) cc_final: 0.8248 (t80) REVERT: B 219 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7755 (t0) REVERT: C 264 MET cc_start: 0.8254 (mmm) cc_final: 0.7674 (mmt) REVERT: D 157 MET cc_start: 0.7589 (mmm) cc_final: 0.7002 (mpp) outliers start: 25 outliers final: 22 residues processed: 103 average time/residue: 0.1381 time to fit residues: 21.9896 Evaluate side-chains 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 45 GLN Chi-restraints excluded: chain A residue 143 THR 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 219 ASP Chi-restraints excluded: chain B residue 251 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 0.0040 chunk 10 optimal weight: 0.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 183 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.106906 restraints weight = 8571.321| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.54 r_work: 0.2956 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7793 Z= 0.124 Angle : 0.487 8.057 10661 Z= 0.249 Chirality : 0.038 0.140 1229 Planarity : 0.004 0.043 1344 Dihedral : 4.346 39.917 1072 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.11 % Allowed : 19.58 % 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: 1.50 (0.27), residues: 1003 helix: 2.06 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 128 HIS 0.001 0.000 HIS C 268 PHE 0.013 0.001 PHE B 225 TYR 0.019 0.001 TYR B 124 ARG 0.002 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 492) hydrogen bonds : angle 3.71218 ( 1458) covalent geometry : bond 0.00290 ( 7793) covalent geometry : angle 0.48722 (10661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.92 seconds wall clock time: 65 minutes 24.78 seconds (3924.78 seconds total)