Starting phenix.real_space_refine on Thu Nov 14 21:55:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_17258.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_17258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_17258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_17258.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/11_2024/8ox6_17258.cif" } resolution = 2.39 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= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 4.55, per 1000 atoms: 0.62 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: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 2.15 Time building geometry restraints manager: 2.27 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: 0.580 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.310 Find NCS groups from input model: 0.070 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- 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 7553 Z= 0.269 Angle : 1.196 70.139 10263 Z= 0.456 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 (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: -0.40 (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 TRP 0.009 0.001 TRP B 260 HIS 0.002 0.000 HIS A 965 PHE 0.019 0.001 PHE A1132 TYR 0.027 0.002 TYR A 968 ARG 0.006 0.000 ARG B 307 *********************** 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 : 0.793 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: 0.8821 time to fit residues: 128.5222 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 : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7553 Z= 0.312 Angle : 0.974 29.922 10263 Z= 0.429 Chirality : 0.047 0.254 1158 Planarity : 0.005 0.039 1273 Dihedral : 8.553 75.053 1088 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.53 % Allowed : 11.25 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.29), residues: 893 helix: 0.52 (0.24), residues: 462 sheet: 1.34 (0.61), residues: 88 loop : -1.19 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS A 167 PHE 0.024 0.002 PHE A1132 TYR 0.017 0.002 TYR A1110 ARG 0.005 0.001 ARG B 307 *********************** 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 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.857 Fit side-chains REVERT: A 875 MET cc_start: 0.5997 (tmm) cc_final: 0.5693 (tmm) REVERT: B 163 ASN cc_start: 0.7907 (t0) cc_final: 0.7701 (t0) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.7505 time to fit residues: 96.3619 Evaluate side-chains 103 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 THR 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 151 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 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 chunk 64 optimal weight: 0.0170 chunk 79 optimal weight: 0.8980 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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** A1138 ASN B 117 ASN B 129 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7553 Z= 0.199 Angle : 0.903 29.532 10263 Z= 0.380 Chirality : 0.043 0.255 1158 Planarity : 0.004 0.034 1273 Dihedral : 6.588 56.292 1088 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.92 % Allowed : 14.16 % Favored : 81.92 % 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: 0.20 (0.29), residues: 893 helix: 0.74 (0.24), residues: 471 sheet: 1.89 (0.61), residues: 82 loop : -1.15 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 207 HIS 0.004 0.001 HIS A 167 PHE 0.013 0.001 PHE A1072 TYR 0.015 0.001 TYR A1110 ARG 0.003 0.000 ARG B 262 *********************** 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 154 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.891 Fit side-chains REVERT: A 875 MET cc_start: 0.5717 (tmm) cc_final: 0.5326 (tmm) REVERT: A 1038 LEU cc_start: 0.8246 (tp) cc_final: 0.7710 (mm) REVERT: B 163 ASN cc_start: 0.7842 (t0) cc_final: 0.7636 (t0) REVERT: B 228 LYS cc_start: 0.6210 (mmpt) cc_final: 0.5927 (mmpt) outliers start: 31 outliers final: 10 residues processed: 140 average time/residue: 0.7272 time to fit residues: 111.4269 Evaluate side-chains 112 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 1133 THR Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 151 LEU 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 60 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.0040 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.198 Angle : 0.898 29.543 10263 Z= 0.375 Chirality : 0.042 0.260 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.777 56.385 1088 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 (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: 0.15 (0.29), residues: 893 helix: 0.75 (0.24), residues: 476 sheet: 1.98 (0.61), residues: 82 loop : -1.33 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1171 HIS 0.002 0.001 HIS A 359 PHE 0.014 0.001 PHE A1132 TYR 0.014 0.001 TYR A 123 ARG 0.003 0.000 ARG B 27 *********************** 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 149 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.798 Fit side-chains REVERT: A 1038 LEU cc_start: 0.8260 (tp) cc_final: 0.7708 (mm) REVERT: A 1057 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: B 228 LYS cc_start: 0.6185 (mmpt) cc_final: 0.5899 (mmpt) outliers start: 30 outliers final: 14 residues processed: 138 average time/residue: 0.7466 time to fit residues: 112.7375 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 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 51 LEU 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 1 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 B 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7553 Z= 0.235 Angle : 0.914 29.541 10263 Z= 0.385 Chirality : 0.044 0.265 1158 Planarity : 0.004 0.036 1273 Dihedral : 5.614 56.449 1088 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.54 % Allowed : 17.07 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.29), residues: 893 helix: 0.78 (0.24), residues: 470 sheet: 1.89 (0.60), residues: 82 loop : -1.36 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.002 0.001 HIS A 939 PHE 0.017 0.001 PHE A1132 TYR 0.018 0.002 TYR A 123 ARG 0.002 0.000 ARG A 412 *********************** 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 143 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.751 Fit side-chains REVERT: A 149 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 1057 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: B 228 LYS cc_start: 0.6086 (mmpt) cc_final: 0.5815 (mmpt) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.7268 time to fit residues: 105.0087 Evaluate side-chains 125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.0070 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.189 Angle : 0.907 29.494 10263 Z= 0.377 Chirality : 0.042 0.260 1158 Planarity : 0.004 0.036 1273 Dihedral : 5.419 56.366 1088 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.29 % Allowed : 17.83 % Favored : 78.89 % 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: 0.27 (0.29), residues: 893 helix: 0.92 (0.24), residues: 470 sheet: 1.93 (0.60), residues: 82 loop : -1.31 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.002 0.000 HIS A 167 PHE 0.015 0.001 PHE A1132 TYR 0.019 0.001 TYR A 123 ARG 0.003 0.000 ARG B 161 *********************** 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 145 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.810 Fit side-chains REVERT: A 427 TYR cc_start: 0.7817 (t80) cc_final: 0.7569 (t80) REVERT: A 1057 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: A 1144 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: B 146 ASP cc_start: 0.5996 (m-30) cc_final: 0.5518 (m-30) REVERT: B 228 LYS cc_start: 0.5928 (mmpt) cc_final: 0.5687 (mmpt) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 0.7922 time to fit residues: 118.2051 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.212 Angle : 0.915 29.433 10263 Z= 0.383 Chirality : 0.042 0.264 1158 Planarity : 0.004 0.037 1273 Dihedral : 5.366 56.364 1088 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.54 % Allowed : 17.70 % Favored : 78.76 % 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: 0.28 (0.29), residues: 893 helix: 0.95 (0.24), residues: 470 sheet: 1.91 (0.59), residues: 82 loop : -1.33 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 207 HIS 0.003 0.001 HIS A 167 PHE 0.013 0.001 PHE A1132 TYR 0.016 0.001 TYR A 123 ARG 0.002 0.000 ARG A 412 *********************** 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 136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.870 Fit side-chains REVERT: A 1057 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: A 1144 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 228 LYS cc_start: 0.5963 (mmpt) cc_final: 0.5728 (mmpt) outliers start: 28 outliers final: 16 residues processed: 125 average time/residue: 0.8159 time to fit residues: 111.6479 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 869 THR Chi-restraints excluded: chain A residue 879 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 59 LEU 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 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.202 Angle : 0.906 29.461 10263 Z= 0.379 Chirality : 0.042 0.263 1158 Planarity : 0.004 0.038 1273 Dihedral : 5.319 56.360 1088 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.41 % Allowed : 18.96 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.29), residues: 893 helix: 0.95 (0.24), residues: 473 sheet: 1.89 (0.59), residues: 82 loop : -1.36 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 207 HIS 0.002 0.000 HIS A 359 PHE 0.012 0.001 PHE A1132 TYR 0.017 0.001 TYR A 123 ARG 0.002 0.000 ARG A 412 *********************** 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 129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.917 Fit side-chains REVERT: A 916 MET cc_start: 0.6883 (tpp) cc_final: 0.6277 (tpp) REVERT: A 1057 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: A 1144 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7865 (m-80) outliers start: 27 outliers final: 17 residues processed: 121 average time/residue: 0.7613 time to fit residues: 101.0589 Evaluate side-chains 117 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 59 LEU 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 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.208 Angle : 0.914 29.488 10263 Z= 0.381 Chirality : 0.042 0.263 1158 Planarity : 0.004 0.038 1273 Dihedral : 5.302 56.338 1088 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.41 % Allowed : 19.22 % 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 (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: 0.28 (0.29), residues: 893 helix: 0.96 (0.24), residues: 473 sheet: 1.89 (0.59), residues: 82 loop : -1.38 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 207 HIS 0.003 0.001 HIS A 167 PHE 0.012 0.001 PHE A1132 TYR 0.021 0.001 TYR A 123 ARG 0.002 0.000 ARG A 412 *********************** 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 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.024 Fit side-chains REVERT: A 916 MET cc_start: 0.6859 (tpp) cc_final: 0.6370 (tpp) REVERT: A 1057 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: A 1144 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7863 (m-80) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 0.8038 time to fit residues: 108.5035 Evaluate side-chains 118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 409 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 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 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 0.0470 chunk 21 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7553 Z= 0.184 Angle : 0.918 29.531 10263 Z= 0.383 Chirality : 0.042 0.260 1158 Planarity : 0.004 0.039 1273 Dihedral : 5.262 56.274 1088 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.53 % Allowed : 20.35 % Favored : 77.12 % 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: 0.32 (0.29), residues: 893 helix: 1.01 (0.24), residues: 472 sheet: 1.90 (0.59), residues: 82 loop : -1.37 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 207 HIS 0.005 0.001 HIS A 167 PHE 0.012 0.001 PHE A1072 TYR 0.024 0.001 TYR A 123 ARG 0.006 0.000 ARG A 166 ********************** 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 124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.847 Fit side-chains REVERT: A 916 MET cc_start: 0.6782 (tpp) cc_final: 0.6348 (tpp) REVERT: A 1057 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: A 1144 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7814 (m-80) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.7753 time to fit residues: 100.1519 Evaluate side-chains 114 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 4 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138928 restraints weight = 9614.541| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.52 r_work: 0.3637 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7553 Z= 0.192 Angle : 0.921 29.543 10263 Z= 0.387 Chirality : 0.042 0.259 1158 Planarity : 0.004 0.039 1273 Dihedral : 5.219 56.249 1088 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.28 % Allowed : 20.35 % 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 (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: 0.39 (0.29), residues: 893 helix: 1.06 (0.24), residues: 473 sheet: 1.96 (0.60), residues: 82 loop : -1.35 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.003 0.000 HIS A 359 PHE 0.015 0.001 PHE A 345 TYR 0.025 0.001 TYR A 123 ARG 0.002 0.000 ARG A 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.43 seconds wall clock time: 50 minutes 11.66 seconds (3011.66 seconds total)