Starting phenix.real_space_refine on Sat Apr 6 06:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/04_2024/8ox6_17258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/04_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_17258/04_2024/8ox6_17258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/04_2024/8ox6_17258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/04_2024/8ox6_17258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox6_17258/04_2024/8ox6_17258_updated.pdb" } 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 Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 897": "OD1" <-> "OD2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.00, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 3.50 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 39 helices and 3 sheets defined 51.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 141 through 173 removed outlier: 3.552A pdb=" N LEU A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.608A pdb=" N VAL A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 154 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A 161 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 172 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 365 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 399 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) removed outlier: 4.924A pdb=" N THR A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N MET A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.599A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 735 through 743 Processing helix chain 'A' and resid 745 through 748 No H-bonds generated for 'chain 'A' and resid 745 through 748' Processing helix chain 'A' and resid 870 through 884 removed outlier: 3.697A pdb=" N VAL A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.244A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 936 Processing helix chain 'A' and resid 939 through 962 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 964 through 971 removed outlier: 3.907A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 988 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) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.655A pdb=" N ILE A1020 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 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 1069 through 1091 Processing helix chain 'A' and resid 1097 through 1118 removed outlier: 3.686A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 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) No H-bonds generated for 'chain 'A' and resid 1120 through 1125' Processing helix chain 'A' and resid 1135 through 1139 Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'B' and resid 50 through 74 Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.738A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 323 through 349 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= A, first strand: chain 'A' and resid 727 through 730 removed outlier: 6.339A pdb=" N ILE A 906 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY A 892 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 908 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'B' and resid 102 through 110 removed outlier: 3.985A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 295 " --> pdb=" O CYS B 104 " (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) 314 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 3.66 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: 89.31 - 107.40: 272 107.40 - 125.49: 9856 125.49 - 143.59: 133 143.59 - 161.68: 0 161.68 - 179.77: 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: 76 2.50 - 3.10: 5998 3.10 - 3.70: 11615 3.70 - 4.30: 17885 4.30 - 4.90: 28712 Nonbonded interactions: 64286 Sorted by model distance: nonbonded pdb=" O ASP A 454 " pdb=" OG1 THR A 458 " model vdw 1.906 2.440 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.939 2.440 nonbonded pdb=" O LEU A 445 " pdb=" OH TYR A1019 " model vdw 1.952 2.440 nonbonded pdb=" O ASN A 989 " pdb=" O HOH A1301 " model vdw 1.991 2.440 nonbonded pdb=" OH TYR B 134 " pdb=" OG SER B 177 " model vdw 1.995 2.440 ... (remaining 64281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.660 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: 3.290 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.390 Find NCS groups from input model: 0.210 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- 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= 0.257 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 fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.752 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: 0.8899 time to fit residues: 129.7609 Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 92 ASN B 117 ASN B 142 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7553 Z= 0.240 Angle : 0.930 30.524 10263 Z= 0.399 Chirality : 0.044 0.255 1158 Planarity : 0.005 0.039 1273 Dihedral : 8.418 75.413 1088 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.35 % 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: -0.23 (0.29), residues: 893 helix: 0.45 (0.24), residues: 457 sheet: 1.25 (0.61), residues: 89 loop : -1.30 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS A 965 PHE 0.024 0.002 PHE A1132 TYR 0.014 0.002 TYR A1110 ARG 0.005 0.001 ARG B 27 *********************** 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 132 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.911 Fit side-chains REVERT: A 875 MET cc_start: 0.5858 (tmm) cc_final: 0.5562 (tmm) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 0.7277 time to fit residues: 96.2594 Evaluate side-chains 109 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 169 MET 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 256 ASP 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: 2.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 79 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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** A1131 GLN B 92 ASN B 117 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7553 Z= 0.230 Angle : 0.896 29.767 10263 Z= 0.376 Chirality : 0.043 0.263 1158 Planarity : 0.004 0.035 1273 Dihedral : 6.963 56.363 1088 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.17 % Allowed : 13.15 % Favored : 82.68 % 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: -0.08 (0.29), residues: 893 helix: 0.55 (0.24), residues: 449 sheet: 1.27 (0.61), residues: 89 loop : -1.14 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.002 0.001 HIS A 965 PHE 0.019 0.001 PHE A1132 TYR 0.016 0.002 TYR A1110 ARG 0.003 0.000 ARG B 307 *********************** 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 147 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 0.966 Fit side-chains REVERT: A 427 TYR cc_start: 0.7959 (t80) cc_final: 0.7708 (t80) REVERT: A 875 MET cc_start: 0.5795 (tmm) cc_final: 0.5420 (tmm) REVERT: A 1014 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6976 (tmm-80) outliers start: 33 outliers final: 12 residues processed: 133 average time/residue: 0.7190 time to fit residues: 104.9497 Evaluate side-chains 118 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 144 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 1014 ARG 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 174 ILE Chi-restraints excluded: chain B residue 256 ASP 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: 0.8980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2140 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= 0.197 Angle : 0.883 29.794 10263 Z= 0.366 Chirality : 0.042 0.261 1158 Planarity : 0.004 0.033 1273 Dihedral : 6.198 56.509 1088 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.54 % Allowed : 15.68 % 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: -0.05 (0.29), residues: 893 helix: 0.53 (0.24), residues: 467 sheet: 1.90 (0.62), residues: 81 loop : -1.27 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 965 PHE 0.015 0.001 PHE A1132 TYR 0.015 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 141 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.795 Fit side-chains REVERT: A 142 TYR cc_start: 0.4850 (m-80) cc_final: 0.4632 (m-80) outliers start: 28 outliers final: 16 residues processed: 130 average time/residue: 0.7646 time to fit residues: 108.4407 Evaluate side-chains 119 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 346 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 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 238 LYS Chi-restraints excluded: chain B residue 256 ASP 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** A1061 GLN B 117 ASN B 142 GLN B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2320 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= 0.231 Angle : 0.894 29.945 10263 Z= 0.373 Chirality : 0.042 0.266 1158 Planarity : 0.004 0.035 1273 Dihedral : 5.878 56.515 1088 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.92 % Allowed : 16.06 % Favored : 80.03 % 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: 0.04 (0.29), residues: 893 helix: 0.60 (0.24), residues: 457 sheet: 1.89 (0.61), residues: 83 loop : -1.17 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.002 0.001 HIS A 939 PHE 0.017 0.001 PHE A1132 TYR 0.012 0.002 TYR A1110 ARG 0.003 0.000 ARG A 118 *********************** 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 136 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.833 Fit side-chains REVERT: A 142 TYR cc_start: 0.4906 (m-80) cc_final: 0.4704 (m-80) REVERT: A 875 MET cc_start: 0.5685 (tmm) cc_final: 0.5454 (tmm) REVERT: A 1038 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 1064 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4707 (mp0) outliers start: 31 outliers final: 16 residues processed: 123 average time/residue: 0.8099 time to fit residues: 108.4744 Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 144 THR 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 1038 LEU 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 42 GLN 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 256 ASP 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: 1.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 933 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7553 Z= 0.249 Angle : 0.901 30.048 10263 Z= 0.376 Chirality : 0.043 0.268 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.692 56.563 1088 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.92 % Allowed : 16.43 % 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 (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: -0.11 (0.29), residues: 893 helix: 0.47 (0.24), residues: 461 sheet: 1.90 (0.61), residues: 83 loop : -1.27 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.003 0.001 HIS A 965 PHE 0.015 0.002 PHE A1132 TYR 0.019 0.002 TYR A1110 ARG 0.002 0.000 ARG A 930 *********************** 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 143 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.842 Fit side-chains REVERT: A 427 TYR cc_start: 0.8005 (t80) cc_final: 0.7740 (t80) REVERT: A 443 GLU cc_start: 0.7755 (pm20) cc_final: 0.7498 (pm20) REVERT: A 1064 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.4712 (mp0) REVERT: B 228 LYS cc_start: 0.6159 (mmpt) cc_final: 0.5935 (mmpt) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.7648 time to fit residues: 107.6996 Evaluate side-chains 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 144 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 888 THR 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 42 GLN 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 256 ASP 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: 0.8980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 933 GLN B 117 ASN B 142 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7553 Z= 0.221 Angle : 0.892 30.012 10263 Z= 0.372 Chirality : 0.042 0.266 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.556 56.468 1088 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.54 % Allowed : 18.71 % Favored : 77.75 % 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: 0.48 (0.24), residues: 463 sheet: 1.83 (0.61), residues: 83 loop : -1.29 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.002 0.001 HIS A 965 PHE 0.013 0.001 PHE A1132 TYR 0.018 0.002 TYR A 123 ARG 0.002 0.000 ARG B 162 *********************** 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 138 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.940 Fit side-chains REVERT: A 1064 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.4730 (mp0) outliers start: 28 outliers final: 18 residues processed: 127 average time/residue: 0.7653 time to fit residues: 106.2684 Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 388 ILE Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 888 THR 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 171 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 256 ASP 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: 3.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 933 GLN B 117 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7553 Z= 0.242 Angle : 0.911 30.109 10263 Z= 0.382 Chirality : 0.043 0.268 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.538 56.472 1088 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.41 % Allowed : 19.34 % Favored : 77.24 % 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: -0.13 (0.29), residues: 893 helix: 0.50 (0.24), residues: 462 sheet: 1.68 (0.60), residues: 83 loop : -1.30 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.002 0.001 HIS A 965 PHE 0.014 0.001 PHE A 345 TYR 0.022 0.002 TYR A 123 ARG 0.002 0.000 ARG A 118 *********************** 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 135 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.948 Fit side-chains REVERT: A 377 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5339 (mp0) REVERT: A 1064 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.4786 (mp0) outliers start: 27 outliers final: 16 residues processed: 126 average time/residue: 0.7575 time to fit residues: 104.4265 Evaluate side-chains 121 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 377 GLU 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 888 THR 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 256 ASP 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: 1.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 933 GLN B 42 GLN B 92 ASN B 117 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7553 Z= 0.316 Angle : 0.933 30.394 10263 Z= 0.400 Chirality : 0.045 0.277 1158 Planarity : 0.004 0.034 1273 Dihedral : 5.632 56.635 1088 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.54 % Allowed : 19.97 % Favored : 76.49 % 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: -0.41 (0.29), residues: 893 helix: 0.32 (0.24), residues: 458 sheet: 0.98 (0.58), residues: 90 loop : -1.38 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 260 HIS 0.003 0.001 HIS A 939 PHE 0.016 0.002 PHE B 179 TYR 0.022 0.002 TYR A 123 ARG 0.003 0.000 ARG A 930 *********************** 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 134 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.790 Fit side-chains REVERT: A 377 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5750 (mp0) REVERT: A 1064 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5009 (mp0) outliers start: 28 outliers final: 14 residues processed: 126 average time/residue: 0.7792 time to fit residues: 107.7421 Evaluate side-chains 121 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 377 GLU 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 888 THR Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1133 THR 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 256 ASP 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: 2.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 933 GLN B 42 GLN B 92 ASN B 117 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.004 0.035 7553 Z= 0.234 Angle : 0.919 30.093 10263 Z= 0.390 Chirality : 0.044 0.264 1158 Planarity : 0.004 0.035 1273 Dihedral : 5.537 56.374 1088 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.91 % Allowed : 21.37 % Favored : 75.73 % 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: -0.30 (0.29), residues: 893 helix: 0.46 (0.24), residues: 458 sheet: 1.03 (0.57), residues: 89 loop : -1.38 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.003 0.001 HIS A 359 PHE 0.018 0.002 PHE A 345 TYR 0.021 0.002 TYR A 123 ARG 0.002 0.000 ARG B 162 ********************** 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 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.856 Fit side-chains REVERT: A 1064 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.4857 (mp0) outliers start: 23 outliers final: 15 residues processed: 121 average time/residue: 0.7672 time to fit residues: 101.8942 Evaluate side-chains 118 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 888 THR Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1167 SER 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 256 ASP 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: 3.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN B 92 ASN B 117 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.168433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133546 restraints weight = 9636.382| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.51 r_work: 0.3570 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2923 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= 0.231 Angle : 0.918 30.070 10263 Z= 0.388 Chirality : 0.043 0.265 1158 Planarity : 0.004 0.035 1273 Dihedral : 5.470 56.315 1088 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.78 % Allowed : 21.49 % Favored : 75.73 % 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: -0.24 (0.29), residues: 893 helix: 0.52 (0.24), residues: 456 sheet: 1.04 (0.57), residues: 89 loop : -1.36 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 359 PHE 0.016 0.001 PHE A 345 TYR 0.021 0.002 TYR A 123 ARG 0.005 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.59 seconds wall clock time: 49 minutes 27.97 seconds (2967.97 seconds total)