Starting phenix.real_space_refine on Fri Aug 22 20:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox6_17258/08_2025/8ox6_17258.map" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 32 5.16 5 C 4817 2.51 5 N 1193 2.21 5 O 1311 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7359 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4643 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 16, 'TRANS': 558} Chain breaks: 3 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.26 Number of scatterers: 7359 At special positions: 0 Unit cell: (71.4288, 93.168, 136.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 32 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1311 8.00 N 1193 7.00 C 4817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 320.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 59.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.844A pdb=" N ASN A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.510A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 174 Proline residue: A 147 - end of helix removed outlier: 4.245A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.569A pdb=" N PHE A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.599A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.557A pdb=" N THR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.697A pdb=" N VAL A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 removed outlier: 3.718A pdb=" N THR A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 937 Processing helix chain 'A' and resid 938 through 963 removed outlier: 3.545A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 removed outlier: 3.907A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 removed outlier: 3.685A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.546A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1057 removed outlier: 3.965A pdb=" N PHE A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1068 through 1092 Processing helix chain 'A' and resid 1097 through 1119 removed outlier: 3.686A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.574A pdb=" N HIS A1123 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1142 through 1156 Processing helix chain 'A' and resid 1157 through 1171 Processing helix chain 'A' and resid 1173 through 1181 removed outlier: 3.638A pdb=" N HIS A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 4.306A pdb=" N ILE B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.634A pdb=" N SER B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.738A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.839A pdb=" N PHE B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 removed outlier: 3.994A pdb=" N ILE B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.579A pdb=" N PHE B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA2, first strand: chain 'A' and resid 727 through 730 removed outlier: 5.996A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 removed outlier: 5.949A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.985A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.985A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.77 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: 2249 1.34 - 1.46: 1944 1.46 - 1.58: 3303 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 7553 Sorted by residual: bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.807 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.791 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 7548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.03: 10257 14.03 - 28.06: 4 28.06 - 42.08: 0 42.08 - 56.11: 0 56.11 - 70.14: 2 Bond angle restraints: 10263 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.82 -70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.77 -70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 89.76 20.45 3.00e+00 1.11e-01 4.65e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 89.31 19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 90.37 19.22 3.00e+00 1.11e-01 4.10e+01 ... (remaining 10258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 4162 21.59 - 43.18: 289 43.18 - 64.77: 24 64.77 - 86.36: 10 86.36 - 107.95: 4 Dihedral angle restraints: 4489 sinusoidal: 1846 harmonic: 2643 Sorted by residual: dihedral pdb=" CA GLN A1131 " pdb=" C GLN A1131 " pdb=" N PHE A1132 " pdb=" CA PHE A1132 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PRO B 90 " pdb=" C PRO B 90 " pdb=" N CYS B 91 " pdb=" CA CYS B 91 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 59.46 33.54 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 4486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 974 0.053 - 0.106: 161 0.106 - 0.159: 22 0.159 - 0.212: 0 0.212 - 0.265: 1 Chirality restraints: 1158 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE A 728 " pdb=" N ILE A 728 " pdb=" C ILE A 728 " pdb=" CB ILE A 728 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1155 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 170 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1126 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A1127 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 217 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 218 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.023 5.00e-02 4.00e+02 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 73 2.50 - 3.10: 5970 3.10 - 3.70: 11576 3.70 - 4.30: 17803 4.30 - 4.90: 28676 Nonbonded interactions: 64098 Sorted by model distance: nonbonded pdb=" O ASP A 454 " pdb=" OG1 THR A 458 " model vdw 1.906 3.040 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.939 3.040 nonbonded pdb=" O LEU A 445 " pdb=" OH TYR A1019 " model vdw 1.952 3.040 nonbonded pdb=" O ASN A 989 " pdb=" O HOH A1301 " model vdw 1.991 3.040 nonbonded pdb=" OH TYR B 134 " pdb=" OG SER B 177 " model vdw 1.995 3.040 ... (remaining 64093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 7561 Z= 0.188 Angle : 1.198 70.139 10284 Z= 0.457 Chirality : 0.040 0.265 1158 Planarity : 0.004 0.045 1273 Dihedral : 14.224 107.953 2784 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 893 helix: 0.28 (0.25), residues: 459 sheet: 1.06 (0.61), residues: 89 loop : -1.31 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 307 TYR 0.027 0.002 TYR A 968 PHE 0.019 0.001 PHE A1132 TRP 0.009 0.001 TRP B 260 HIS 0.002 0.000 HIS A 965 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7553) covalent geometry : angle 1.19609 (10263) SS BOND : bond 0.00525 ( 3) SS BOND : angle 1.45719 ( 6) hydrogen bonds : bond 0.26504 ( 361) hydrogen bonds : angle 8.62547 ( 1026) link_BETA1-4 : bond 0.01095 ( 2) link_BETA1-4 : angle 2.39476 ( 6) link_NAG-ASN : bond 0.00090 ( 3) link_NAG-ASN : angle 1.75030 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 981 GLU cc_start: 0.7977 (tt0) cc_final: 0.7447 (tt0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3725 time to fit residues: 54.1516 Evaluate side-chains 96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN B 117 ASN B 142 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.171703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136185 restraints weight = 9715.210| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.56 r_work: 0.3602 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7561 Z= 0.185 Angle : 0.961 31.031 10284 Z= 0.418 Chirality : 0.045 0.251 1158 Planarity : 0.005 0.040 1273 Dihedral : 8.397 72.985 1088 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.53 % Allowed : 11.00 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.29), residues: 893 helix: 0.58 (0.24), residues: 463 sheet: 1.35 (0.61), residues: 88 loop : -1.17 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 27 TYR 0.015 0.002 TYR A1110 PHE 0.022 0.002 PHE A1132 TRP 0.012 0.001 TRP B 260 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7553) covalent geometry : angle 0.95852 (10263) SS BOND : bond 0.00339 ( 3) SS BOND : angle 1.36244 ( 6) hydrogen bonds : bond 0.06015 ( 361) hydrogen bonds : angle 5.75077 ( 1026) link_BETA1-4 : bond 0.01862 ( 2) link_BETA1-4 : angle 2.65431 ( 6) link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 1.56339 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.183 Fit side-chains REVERT: A 427 TYR cc_start: 0.7778 (t80) cc_final: 0.7481 (t80) REVERT: A 875 MET cc_start: 0.5292 (tmm) cc_final: 0.4970 (tmm) outliers start: 20 outliers final: 7 residues processed: 123 average time/residue: 0.2785 time to fit residues: 37.5363 Evaluate side-chains 103 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 GLN B 117 ASN B 129 GLN B 144 ASN B 235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.172836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137602 restraints weight = 9691.734| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.54 r_work: 0.3616 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7561 Z= 0.151 Angle : 0.915 29.568 10284 Z= 0.387 Chirality : 0.044 0.261 1158 Planarity : 0.004 0.035 1273 Dihedral : 6.613 56.295 1088 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.55 % Allowed : 13.02 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.29), residues: 893 helix: 0.72 (0.24), residues: 471 sheet: 1.47 (0.60), residues: 88 loop : -1.18 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.016 0.002 TYR A1110 PHE 0.013 0.001 PHE A1132 TRP 0.010 0.001 TRP B 207 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7553) covalent geometry : angle 0.91189 (10263) SS BOND : bond 0.00339 ( 3) SS BOND : angle 1.36828 ( 6) hydrogen bonds : bond 0.04846 ( 361) hydrogen bonds : angle 5.16180 ( 1026) link_BETA1-4 : bond 0.01687 ( 2) link_BETA1-4 : angle 2.66681 ( 6) link_NAG-ASN : bond 0.00049 ( 3) link_NAG-ASN : angle 1.75616 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.263 Fit side-chains REVERT: A 427 TYR cc_start: 0.7734 (t80) cc_final: 0.7366 (t80) REVERT: A 875 MET cc_start: 0.5106 (tmm) cc_final: 0.4615 (tmm) REVERT: A 983 TRP cc_start: 0.7749 (m100) cc_final: 0.7524 (m100) REVERT: A 1038 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7396 (mm) REVERT: A 1057 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6287 (mp10) REVERT: A 1140 LEU cc_start: 0.8065 (mt) cc_final: 0.7835 (mm) REVERT: B 29 ASP cc_start: 0.7381 (t0) cc_final: 0.7140 (t0) REVERT: B 129 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: B 228 LYS cc_start: 0.6848 (mmpt) cc_final: 0.6217 (mmpt) outliers start: 36 outliers final: 10 residues processed: 140 average time/residue: 0.3028 time to fit residues: 46.2397 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.171653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136285 restraints weight = 9845.175| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.55 r_work: 0.3599 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7561 Z= 0.158 Angle : 0.915 29.501 10284 Z= 0.384 Chirality : 0.043 0.263 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.972 56.450 1088 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.79 % Allowed : 15.42 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.29), residues: 893 helix: 0.74 (0.24), residues: 469 sheet: 1.92 (0.61), residues: 82 loop : -1.22 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.018 0.002 TYR A 123 PHE 0.019 0.001 PHE B 179 TRP 0.010 0.001 TRP B 260 HIS 0.002 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7553) covalent geometry : angle 0.91101 (10263) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.37969 ( 6) hydrogen bonds : bond 0.04565 ( 361) hydrogen bonds : angle 5.04129 ( 1026) link_BETA1-4 : bond 0.01764 ( 2) link_BETA1-4 : angle 2.77067 ( 6) link_NAG-ASN : bond 0.00044 ( 3) link_NAG-ASN : angle 1.72533 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.284 Fit side-chains REVERT: A 875 MET cc_start: 0.5439 (tmm) cc_final: 0.5187 (tmm) REVERT: A 983 TRP cc_start: 0.7809 (m100) cc_final: 0.7560 (m100) REVERT: A 1057 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6314 (mp10) REVERT: A 1140 LEU cc_start: 0.8099 (mt) cc_final: 0.7862 (mm) REVERT: A 1178 ILE cc_start: 0.7371 (pt) cc_final: 0.7149 (pp) REVERT: B 29 ASP cc_start: 0.7364 (t0) cc_final: 0.7034 (t0) REVERT: B 165 ASP cc_start: 0.7557 (p0) cc_final: 0.7097 (m-30) REVERT: B 228 LYS cc_start: 0.6851 (mmpt) cc_final: 0.6260 (mmpt) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 0.3038 time to fit residues: 45.7094 Evaluate side-chains 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.171755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136622 restraints weight = 9783.828| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.54 r_work: 0.3605 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7561 Z= 0.147 Angle : 0.907 29.452 10284 Z= 0.379 Chirality : 0.042 0.263 1158 Planarity : 0.004 0.036 1273 Dihedral : 5.687 56.437 1088 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 17.19 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.29), residues: 893 helix: 0.86 (0.24), residues: 465 sheet: 1.93 (0.61), residues: 82 loop : -1.22 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 27 TYR 0.018 0.002 TYR A 123 PHE 0.017 0.001 PHE A1132 TRP 0.011 0.001 TRP B 207 HIS 0.002 0.001 HIS A 965 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7553) covalent geometry : angle 0.90289 (10263) SS BOND : bond 0.00263 ( 3) SS BOND : angle 1.35747 ( 6) hydrogen bonds : bond 0.04398 ( 361) hydrogen bonds : angle 4.93587 ( 1026) link_BETA1-4 : bond 0.01726 ( 2) link_BETA1-4 : angle 2.83735 ( 6) link_NAG-ASN : bond 0.00044 ( 3) link_NAG-ASN : angle 1.70419 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.282 Fit side-chains REVERT: A 149 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 427 TYR cc_start: 0.7785 (t80) cc_final: 0.7539 (t80) REVERT: A 716 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: A 875 MET cc_start: 0.5187 (tmm) cc_final: 0.4897 (tmm) REVERT: A 983 TRP cc_start: 0.7814 (m100) cc_final: 0.7571 (m100) REVERT: A 1057 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6075 (mp10) REVERT: A 1114 MET cc_start: 0.7399 (ttp) cc_final: 0.7025 (ttm) REVERT: A 1140 LEU cc_start: 0.8110 (mt) cc_final: 0.7881 (mm) REVERT: A 1178 ILE cc_start: 0.7508 (pt) cc_final: 0.7246 (pp) REVERT: B 29 ASP cc_start: 0.7430 (t0) cc_final: 0.7044 (t0) REVERT: B 165 ASP cc_start: 0.7413 (p0) cc_final: 0.7110 (m-30) REVERT: B 228 LYS cc_start: 0.6732 (mmpt) cc_final: 0.6162 (mmpt) REVERT: B 270 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8131 (ptp-170) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.3469 time to fit residues: 50.4474 Evaluate side-chains 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN A1061 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135837 restraints weight = 9698.560| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.53 r_work: 0.3594 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7561 Z= 0.148 Angle : 0.910 29.490 10284 Z= 0.380 Chirality : 0.042 0.264 1158 Planarity : 0.004 0.037 1273 Dihedral : 5.536 56.435 1088 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.67 % Allowed : 18.46 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.29), residues: 893 helix: 0.88 (0.24), residues: 470 sheet: 1.97 (0.61), residues: 82 loop : -1.36 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.019 0.002 TYR A 123 PHE 0.017 0.001 PHE B 179 TRP 0.010 0.001 TRP B 260 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7553) covalent geometry : angle 0.90619 (10263) SS BOND : bond 0.00279 ( 3) SS BOND : angle 1.36548 ( 6) hydrogen bonds : bond 0.04323 ( 361) hydrogen bonds : angle 4.84171 ( 1026) link_BETA1-4 : bond 0.01751 ( 2) link_BETA1-4 : angle 2.89967 ( 6) link_NAG-ASN : bond 0.00030 ( 3) link_NAG-ASN : angle 1.66533 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.290 Fit side-chains REVERT: A 145 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7071 (tp) REVERT: A 427 TYR cc_start: 0.7783 (t80) cc_final: 0.7533 (t80) REVERT: A 875 MET cc_start: 0.5107 (tmm) cc_final: 0.4709 (tmm) REVERT: A 983 TRP cc_start: 0.7789 (m100) cc_final: 0.7514 (m100) REVERT: A 1038 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7427 (mm) REVERT: A 1057 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6052 (mp10) REVERT: A 1140 LEU cc_start: 0.8123 (mt) cc_final: 0.7875 (mm) REVERT: A 1178 ILE cc_start: 0.7528 (pt) cc_final: 0.7258 (pp) REVERT: B 29 ASP cc_start: 0.7403 (t0) cc_final: 0.7068 (t0) REVERT: B 146 ASP cc_start: 0.6526 (m-30) cc_final: 0.6235 (m-30) REVERT: B 165 ASP cc_start: 0.7454 (p0) cc_final: 0.7044 (m-30) REVERT: B 228 LYS cc_start: 0.6719 (mmpt) cc_final: 0.6162 (mmpt) REVERT: B 246 ASP cc_start: 0.6981 (t0) cc_final: 0.6680 (t0) REVERT: B 270 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8127 (ptp-170) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 0.3655 time to fit residues: 54.6068 Evaluate side-chains 133 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.172469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137192 restraints weight = 9773.460| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.53 r_work: 0.3612 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7561 Z= 0.131 Angle : 0.903 29.443 10284 Z= 0.375 Chirality : 0.042 0.261 1158 Planarity : 0.004 0.038 1273 Dihedral : 5.374 56.333 1088 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.41 % Allowed : 18.71 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.29), residues: 893 helix: 0.94 (0.24), residues: 472 sheet: 1.86 (0.60), residues: 82 loop : -1.39 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.019 0.001 TYR A1110 PHE 0.015 0.001 PHE B 179 TRP 0.012 0.001 TRP B 207 HIS 0.003 0.000 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7553) covalent geometry : angle 0.89963 (10263) SS BOND : bond 0.00279 ( 3) SS BOND : angle 1.30312 ( 6) hydrogen bonds : bond 0.04133 ( 361) hydrogen bonds : angle 4.73242 ( 1026) link_BETA1-4 : bond 0.01657 ( 2) link_BETA1-4 : angle 2.76637 ( 6) link_NAG-ASN : bond 0.00030 ( 3) link_NAG-ASN : angle 1.59922 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.222 Fit side-chains REVERT: A 122 LEU cc_start: 0.7155 (pp) cc_final: 0.6866 (pp) REVERT: A 427 TYR cc_start: 0.7762 (t80) cc_final: 0.7557 (t80) REVERT: A 875 MET cc_start: 0.5345 (tmm) cc_final: 0.4703 (tmm) REVERT: A 879 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6811 (mp) REVERT: A 983 TRP cc_start: 0.7786 (m100) cc_final: 0.7543 (m100) REVERT: A 1057 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6032 (mp10) REVERT: A 1106 SER cc_start: 0.8143 (m) cc_final: 0.7936 (m) REVERT: A 1114 MET cc_start: 0.7285 (ttp) cc_final: 0.7039 (ttm) REVERT: A 1140 LEU cc_start: 0.8079 (mt) cc_final: 0.7865 (mm) REVERT: B 29 ASP cc_start: 0.7423 (t0) cc_final: 0.7085 (t0) REVERT: B 228 LYS cc_start: 0.6628 (mmpt) cc_final: 0.5978 (mmpt) REVERT: B 246 ASP cc_start: 0.6983 (t0) cc_final: 0.6685 (t0) REVERT: B 270 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8067 (ptp-170) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 0.3405 time to fit residues: 51.4017 Evaluate side-chains 129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.0770 chunk 59 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135286 restraints weight = 9851.823| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.52 r_work: 0.3587 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7561 Z= 0.158 Angle : 0.924 29.514 10284 Z= 0.386 Chirality : 0.043 0.267 1158 Planarity : 0.004 0.038 1273 Dihedral : 5.380 56.412 1088 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.54 % Allowed : 19.09 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.29), residues: 893 helix: 0.98 (0.24), residues: 467 sheet: 1.77 (0.59), residues: 82 loop : -1.25 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.020 0.002 TYR A1110 PHE 0.018 0.001 PHE B 179 TRP 0.013 0.001 TRP B 207 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7553) covalent geometry : angle 0.91974 (10263) SS BOND : bond 0.00241 ( 3) SS BOND : angle 1.36730 ( 6) hydrogen bonds : bond 0.04274 ( 361) hydrogen bonds : angle 4.76219 ( 1026) link_BETA1-4 : bond 0.01637 ( 2) link_BETA1-4 : angle 2.95702 ( 6) link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 1.68857 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.253 Fit side-chains REVERT: A 875 MET cc_start: 0.5330 (tmm) cc_final: 0.4667 (tmm) REVERT: A 879 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7010 (mp) REVERT: A 916 MET cc_start: 0.7300 (tpp) cc_final: 0.6969 (tpp) REVERT: A 983 TRP cc_start: 0.7828 (m100) cc_final: 0.7570 (m100) REVERT: A 1057 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: A 1064 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.4678 (mp0) REVERT: A 1106 SER cc_start: 0.8208 (m) cc_final: 0.7996 (m) REVERT: A 1114 MET cc_start: 0.7305 (ttp) cc_final: 0.7046 (ttm) REVERT: A 1140 LEU cc_start: 0.8102 (mt) cc_final: 0.7886 (mm) REVERT: B 29 ASP cc_start: 0.7429 (t0) cc_final: 0.7108 (t0) REVERT: B 228 LYS cc_start: 0.6656 (mmpt) cc_final: 0.6121 (mmpt) REVERT: B 246 ASP cc_start: 0.6990 (t0) cc_final: 0.6683 (t0) REVERT: B 270 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (ptp-170) outliers start: 28 outliers final: 15 residues processed: 130 average time/residue: 0.3248 time to fit residues: 46.0964 Evaluate side-chains 126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131255 restraints weight = 9711.149| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.51 r_work: 0.3535 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7561 Z= 0.235 Angle : 0.965 29.819 10284 Z= 0.414 Chirality : 0.046 0.276 1158 Planarity : 0.004 0.039 1273 Dihedral : 5.562 56.582 1088 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.54 % Allowed : 19.47 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.29), residues: 893 helix: 0.69 (0.24), residues: 464 sheet: 1.15 (0.57), residues: 88 loop : -1.39 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.033 0.002 TYR A 123 PHE 0.021 0.002 PHE B 179 TRP 0.015 0.002 TRP B 260 HIS 0.011 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 7553) covalent geometry : angle 0.96105 (10263) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.64968 ( 6) hydrogen bonds : bond 0.04802 ( 361) hydrogen bonds : angle 4.97317 ( 1026) link_BETA1-4 : bond 0.01619 ( 2) link_BETA1-4 : angle 3.16999 ( 6) link_NAG-ASN : bond 0.00300 ( 3) link_NAG-ASN : angle 1.80438 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.281 Fit side-chains REVERT: A 875 MET cc_start: 0.5659 (tmm) cc_final: 0.4913 (tmm) REVERT: A 879 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6741 (mp) REVERT: A 983 TRP cc_start: 0.7956 (m100) cc_final: 0.7754 (m100) REVERT: A 1057 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: A 1064 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5032 (mp0) REVERT: A 1114 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7034 (ttm) REVERT: B 29 ASP cc_start: 0.7460 (t0) cc_final: 0.7114 (t0) REVERT: B 228 LYS cc_start: 0.6759 (mmpt) cc_final: 0.6237 (mmpt) REVERT: B 246 ASP cc_start: 0.6948 (t0) cc_final: 0.6630 (t0) REVERT: B 270 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8139 (ptp-170) outliers start: 28 outliers final: 14 residues processed: 129 average time/residue: 0.3557 time to fit residues: 49.8045 Evaluate side-chains 126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN B 117 ASN ** B 144 ASN ** 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 = 0.4109 r_free = 0.4109 target = 0.168739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133373 restraints weight = 9704.017| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.48 r_work: 0.3581 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7561 Z= 0.150 Angle : 0.923 29.458 10284 Z= 0.390 Chirality : 0.043 0.261 1158 Planarity : 0.004 0.039 1273 Dihedral : 5.443 56.330 1088 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.91 % Allowed : 20.35 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.29), residues: 893 helix: 0.89 (0.24), residues: 463 sheet: 1.23 (0.57), residues: 88 loop : -1.31 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.030 0.002 TYR A 123 PHE 0.024 0.001 PHE A 345 TRP 0.017 0.001 TRP B 207 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7553) covalent geometry : angle 0.91934 (10263) SS BOND : bond 0.00285 ( 3) SS BOND : angle 1.41312 ( 6) hydrogen bonds : bond 0.04307 ( 361) hydrogen bonds : angle 4.80611 ( 1026) link_BETA1-4 : bond 0.01605 ( 2) link_BETA1-4 : angle 2.80305 ( 6) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.62202 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.286 Fit side-chains REVERT: A 377 GLU cc_start: 0.7145 (mp0) cc_final: 0.6799 (pt0) REVERT: A 875 MET cc_start: 0.5440 (tmm) cc_final: 0.4774 (tmm) REVERT: A 879 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6694 (mp) REVERT: A 983 TRP cc_start: 0.7876 (m100) cc_final: 0.7671 (m100) REVERT: A 1057 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6186 (mp10) REVERT: A 1064 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.4672 (mp0) REVERT: A 1114 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7043 (ttm) REVERT: A 1140 LEU cc_start: 0.8137 (mt) cc_final: 0.7916 (mm) REVERT: B 29 ASP cc_start: 0.7439 (t0) cc_final: 0.7140 (t0) REVERT: B 228 LYS cc_start: 0.6572 (mmpt) cc_final: 0.6030 (mmtt) REVERT: B 246 ASP cc_start: 0.6889 (t0) cc_final: 0.6564 (t0) REVERT: B 270 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8078 (ptp-170) outliers start: 23 outliers final: 13 residues processed: 122 average time/residue: 0.3575 time to fit residues: 47.2602 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN B 117 ASN ** B 144 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.172049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136992 restraints weight = 9753.223| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.52 r_work: 0.3608 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7561 Z= 0.132 Angle : 0.929 29.521 10284 Z= 0.389 Chirality : 0.043 0.257 1158 Planarity : 0.004 0.039 1273 Dihedral : 5.303 56.178 1088 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.28 % Allowed : 21.37 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.29), residues: 893 helix: 1.01 (0.24), residues: 466 sheet: 1.24 (0.57), residues: 88 loop : -1.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.026 0.002 TYR A 123 PHE 0.027 0.001 PHE A 345 TRP 0.020 0.001 TRP B 207 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7553) covalent geometry : angle 0.92605 (10263) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.30415 ( 6) hydrogen bonds : bond 0.04066 ( 361) hydrogen bonds : angle 4.67883 ( 1026) link_BETA1-4 : bond 0.01446 ( 2) link_BETA1-4 : angle 2.56109 ( 6) link_NAG-ASN : bond 0.00047 ( 3) link_NAG-ASN : angle 1.51438 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.64 seconds wall clock time: 44 minutes 1.97 seconds (2641.97 seconds total)