Starting phenix.real_space_refine on Wed Aug 5 19:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2026/8c5u_16443.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 35 5.16 5 C 7075 2.51 5 N 1984 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11419 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2698 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7224 Classifications: {'peptide': 919} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 44, 'TRANS': 874} Chain breaks: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 9, 'ASP:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 663 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 152 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.06, per 1000 atoms: 0.18 Number of scatterers: 11419 At special positions: 0 Unit cell: (105.73, 117.37, 118.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 74 15.00 O 2251 8.00 N 1984 7.00 C 7075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 488.7 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 60.3% alpha, 7.5% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.939A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.867A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.785A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.623A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.663A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 234' Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.230A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.610A pdb=" N MET B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 4.500A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 449 through 478 Proline residue: A 463 - end of helix removed outlier: 3.831A pdb=" N GLU A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.905A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.664A pdb=" N LYS A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.831A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 removed outlier: 3.654A pdb=" N VAL A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 663 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.568A pdb=" N VAL A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 814 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 873 removed outlier: 4.443A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.615A pdb=" N GLN A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 997 Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.055A pdb=" N VAL A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1039 through 1041 No H-bonds generated for 'chain 'A' and resid 1039 through 1041' Processing helix chain 'A' and resid 1047 through 1066 Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.539A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1293 removed outlier: 3.501A pdb=" N ARG A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A1288 " --> pdb=" O ILE A1284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A1289 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.584A pdb=" N LEU A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A1300 " --> pdb=" O THR A1296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1295 through 1300' Processing helix chain 'A' and resid 1305 through 1310 removed outlier: 3.558A pdb=" N LEU A1309 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1346 Processing sheet with id=AA1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.949A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 50 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU B 76 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP B 52 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA8, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1128 through 1131 removed outlier: 3.679A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2672 1.33 - 1.45: 2719 1.45 - 1.57: 6243 1.57 - 1.69: 141 1.69 - 1.81: 60 Bond restraints: 11835 Sorted by residual: bond pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 1.607 1.704 -0.097 1.20e-02 6.94e+03 6.59e+01 bond pdb=" C1' DA N 132 " pdb=" N9 DA N 132 " ideal model delta sigma weight residual 1.468 1.374 0.094 1.40e-02 5.10e+03 4.55e+01 bond pdb=" C1' DT N 134 " pdb=" N1 DT N 134 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" C1' DT T 15 " pdb=" N1 DT T 15 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" O3' DC T 11 " pdb=" P DA T 12 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.20e-02 6.94e+03 2.16e+01 ... (remaining 11830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16174 3.01 - 6.01: 155 6.01 - 9.02: 13 9.02 - 12.02: 4 12.02 - 15.03: 2 Bond angle restraints: 16348 Sorted by residual: angle pdb=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 119.70 112.88 6.82 1.20e+00 6.94e-01 3.23e+01 angle pdb=" C5' DC T 25 " pdb=" C4' DC T 25 " pdb=" O4' DC T 25 " ideal model delta sigma weight residual 109.30 118.99 -9.69 1.90e+00 2.77e-01 2.60e+01 angle pdb=" C TYR A 499 " pdb=" CA TYR A 499 " pdb=" CB TYR A 499 " ideal model delta sigma weight residual 110.44 101.95 8.49 1.68e+00 3.54e-01 2.55e+01 angle pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sigma weight residual 120.50 135.53 -15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" PB GTP C 201 " pdb=" O3B GTP C 201 " pdb=" PG GTP C 201 " ideal model delta sigma weight residual 120.50 132.88 -12.38 3.00e+00 1.11e-01 1.70e+01 ... (remaining 16343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 6473 29.60 - 59.19: 443 59.19 - 88.78: 33 88.78 - 118.38: 3 118.38 - 147.97: 4 Dihedral angle restraints: 6956 sinusoidal: 3312 harmonic: 3644 Sorted by residual: dihedral pdb=" O4' G C 108 " pdb=" C2' G C 108 " pdb=" C1' G C 108 " pdb=" C3' G C 108 " ideal model delta sinusoidal sigma weight residual 25.59 -9.47 35.06 3 3.80e+00 6.93e-02 9.32e+01 dihedral pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " pdb=" C1' G C 108 " ideal model delta sinusoidal sigma weight residual 36.34 13.18 23.16 1 3.10e+00 1.04e-01 8.05e+01 dihedral pdb=" C4' G C 108 " pdb=" O4' G C 108 " pdb=" C1' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 3.88 -30.39 34.27 3 5.00e+00 4.00e-02 5.21e+01 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1758 0.127 - 0.254: 47 0.254 - 0.381: 4 0.381 - 0.508: 0 0.508 - 0.636: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" P G C 102 " pdb=" OP1 G C 102 " pdb=" OP2 G C 102 " pdb=" O5' G C 102 " both_signs ideal model delta sigma weight residual True 2.17 2.81 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DT T 41 " pdb=" OP1 DT T 41 " pdb=" OP2 DT T 41 " pdb=" O5' DT T 41 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" P DT N 111 " pdb=" OP1 DT N 111 " pdb=" OP2 DT N 111 " pdb=" O5' DT N 111 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 1809 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1350 " -0.008 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE A1350 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A1350 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A1350 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1350 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1350 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A1350 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1337 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C ASP A1337 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP A1337 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A1338 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 15 " 0.016 2.00e-02 2.50e+03 8.85e-03 1.96e+00 pdb=" N1 DT T 15 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DT T 15 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT T 15 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT T 15 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT T 15 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT T 15 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT T 15 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT T 15 " -0.010 2.00e-02 2.50e+03 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 751 2.73 - 3.27: 11289 3.27 - 3.82: 19694 3.82 - 4.36: 22850 4.36 - 4.90: 37585 Nonbonded interactions: 92169 Sorted by model distance: nonbonded pdb=" OD1 ASN A 842 " pdb=" OG SER A 845 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.206 3.040 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU A1125 " pdb=" OG SER A1140 " model vdw 2.281 3.040 nonbonded pdb=" OG SER B 124 " pdb=" OD1 ASP B 126 " model vdw 2.307 3.040 ... (remaining 92164 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.130 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.097 11836 Z= 0.304 Angle : 0.748 15.031 16348 Z= 0.432 Chirality : 0.056 0.636 1812 Planarity : 0.004 0.034 1833 Dihedral : 18.275 147.972 4594 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1238 helix: 1.75 (0.20), residues: 677 sheet: -0.61 (0.49), residues: 110 loop : -0.42 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1151 TYR 0.016 0.001 TYR A 496 PHE 0.028 0.001 PHE A1350 TRP 0.012 0.001 TRP B 159 HIS 0.007 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.30 (11835) covalent geometry : angle 0.74835 / 0.43 (16348) hydrogen bonds : bond 0.14963 / 9.52 ( 595) hydrogen bonds : angle 5.94133 / 4.06 ( 1642) Misc. bond : bond 0.06276 / 3.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 39 THR cc_start: 0.8684 (p) cc_final: 0.8133 (t) REVERT: B 209 ASP cc_start: 0.8343 (t0) cc_final: 0.8111 (t0) REVERT: B 329 MET cc_start: 0.7504 (tpp) cc_final: 0.7055 (tpp) REVERT: A 796 ASP cc_start: 0.8136 (m-30) cc_final: 0.7779 (m-30) REVERT: A 926 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 962 GLU cc_start: 0.8024 (tp30) cc_final: 0.7771 (tp30) REVERT: A 1007 LYS cc_start: 0.7761 (pttt) cc_final: 0.7501 (pttt) REVERT: A 1197 ASP cc_start: 0.8267 (m-30) cc_final: 0.8063 (m-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0910 time to fit residues: 23.2093 Evaluate side-chains 137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 308 ASN A 791 ASN A 925 ASN A1070 HIS A1129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094657 restraints weight = 20889.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097693 restraints weight = 11263.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099655 restraints weight = 7964.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100878 restraints weight = 6513.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101501 restraints weight = 5798.538| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11836 Z= 0.190 Angle : 0.642 9.582 16348 Z= 0.347 Chirality : 0.044 0.193 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.252 150.928 2175 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.41 % Allowed : 8.06 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1238 helix: 1.75 (0.20), residues: 676 sheet: -0.60 (0.45), residues: 124 loop : -0.43 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1328 TYR 0.023 0.001 TYR A 496 PHE 0.021 0.001 PHE A1350 TRP 0.018 0.001 TRP A 908 HIS 0.004 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (11835) covalent geometry : angle 0.64243 / 0.35 (16348) hydrogen bonds : bond 0.05244 / 3.34 ( 595) hydrogen bonds : angle 4.50477 / 3.05 ( 1642) Misc. bond : bond 0.00105 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 131 LYS cc_start: 0.8294 (mptt) cc_final: 0.8036 (mppt) REVERT: B 209 ASP cc_start: 0.8300 (t0) cc_final: 0.8014 (t0) REVERT: B 329 MET cc_start: 0.7553 (tpp) cc_final: 0.7094 (tpp) REVERT: A 533 ARG cc_start: 0.8607 (ptp90) cc_final: 0.8352 (ttp-170) REVERT: A 796 ASP cc_start: 0.8191 (m-30) cc_final: 0.7880 (m-30) REVERT: A 905 ASP cc_start: 0.8169 (m-30) cc_final: 0.7902 (t0) REVERT: A 962 GLU cc_start: 0.8043 (tp30) cc_final: 0.7708 (tp30) REVERT: A 1078 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 1197 ASP cc_start: 0.8384 (m-30) cc_final: 0.8176 (m-30) REVERT: A 1259 LEU cc_start: 0.8239 (tt) cc_final: 0.7695 (mt) outliers start: 15 outliers final: 11 residues processed: 155 average time/residue: 0.0876 time to fit residues: 19.7592 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 128 optimal weight: 40.0000 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 127 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 HIS B 72 GLN B 308 ASN A1036 GLN A1070 HIS A1129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094202 restraints weight = 21081.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097270 restraints weight = 11348.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099253 restraints weight = 8017.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100390 restraints weight = 6546.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101073 restraints weight = 5842.263| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11836 Z= 0.173 Angle : 0.601 8.823 16348 Z= 0.325 Chirality : 0.043 0.188 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.259 156.960 2175 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 9.37 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1238 helix: 1.73 (0.20), residues: 678 sheet: -0.62 (0.45), residues: 124 loop : -0.48 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.025 0.001 TYR A 496 PHE 0.023 0.001 PHE A1350 TRP 0.021 0.001 TRP A 908 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (11835) covalent geometry : angle 0.60102 / 0.32 (16348) hydrogen bonds : bond 0.04427 / 2.83 ( 595) hydrogen bonds : angle 4.34001 / 2.94 ( 1642) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 209 ASP cc_start: 0.8230 (t0) cc_final: 0.7931 (t0) REVERT: B 329 MET cc_start: 0.7613 (tpp) cc_final: 0.7262 (tpp) REVERT: A 533 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8378 (ttp-170) REVERT: A 796 ASP cc_start: 0.8216 (m-30) cc_final: 0.7932 (m-30) REVERT: A 905 ASP cc_start: 0.8156 (m-30) cc_final: 0.7883 (t0) REVERT: A 962 GLU cc_start: 0.8041 (tp30) cc_final: 0.7719 (tp30) REVERT: A 1015 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 1078 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 1259 LEU cc_start: 0.8170 (tt) cc_final: 0.7569 (mp) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.0862 time to fit residues: 19.3502 Evaluate side-chains 140 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 126 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 275 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A 925 ASN A1070 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093535 restraints weight = 20966.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096667 restraints weight = 11249.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098697 restraints weight = 7936.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099928 restraints weight = 6480.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100603 restraints weight = 5777.739| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11836 Z= 0.175 Angle : 0.609 12.276 16348 Z= 0.325 Chirality : 0.043 0.207 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.225 162.099 2175 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.34 % Allowed : 11.81 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1238 helix: 1.71 (0.20), residues: 679 sheet: -0.64 (0.45), residues: 128 loop : -0.49 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 533 TYR 0.026 0.001 TYR B 161 PHE 0.018 0.001 PHE A1350 TRP 0.021 0.001 TRP A 908 HIS 0.004 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11835) covalent geometry : angle 0.60853 / 0.32 (16348) hydrogen bonds : bond 0.04287 / 2.73 ( 595) hydrogen bonds : angle 4.29759 / 2.93 ( 1642) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 209 ASP cc_start: 0.8223 (t0) cc_final: 0.7900 (t0) REVERT: B 329 MET cc_start: 0.7596 (tpp) cc_final: 0.7233 (tpp) REVERT: A 533 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8339 (ttp-170) REVERT: A 796 ASP cc_start: 0.8250 (m-30) cc_final: 0.7920 (m-30) REVERT: A 905 ASP cc_start: 0.8139 (m-30) cc_final: 0.7908 (t0) REVERT: A 962 GLU cc_start: 0.8095 (tp30) cc_final: 0.7759 (tp30) REVERT: A 1078 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 1259 LEU cc_start: 0.8108 (tt) cc_final: 0.7579 (mp) REVERT: A 1278 LEU cc_start: 0.7736 (mp) cc_final: 0.7415 (tp) outliers start: 25 outliers final: 14 residues processed: 148 average time/residue: 0.0890 time to fit residues: 19.0973 Evaluate side-chains 141 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093916 restraints weight = 20872.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097083 restraints weight = 11212.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099095 restraints weight = 7882.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100344 restraints weight = 6455.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100763 restraints weight = 5747.152| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11836 Z= 0.155 Angle : 0.584 8.435 16348 Z= 0.314 Chirality : 0.042 0.230 1812 Planarity : 0.003 0.035 1833 Dihedral : 20.166 170.480 2175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.44 % Allowed : 12.09 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1238 helix: 1.74 (0.20), residues: 683 sheet: -0.61 (0.45), residues: 128 loop : -0.49 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.013 0.001 TYR A 496 PHE 0.015 0.001 PHE A1350 TRP 0.023 0.001 TRP A 908 HIS 0.003 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (11835) covalent geometry : angle 0.58360 / 0.31 (16348) hydrogen bonds : bond 0.04074 / 2.60 ( 595) hydrogen bonds : angle 4.21570 / 2.87 ( 1642) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5680 (tt0) cc_final: 0.5420 (tt0) REVERT: B 141 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 209 ASP cc_start: 0.8212 (t0) cc_final: 0.7895 (t0) REVERT: B 329 MET cc_start: 0.7614 (tpp) cc_final: 0.7222 (tpp) REVERT: A 533 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8409 (ttp-170) REVERT: A 796 ASP cc_start: 0.8231 (m-30) cc_final: 0.7854 (m-30) REVERT: A 905 ASP cc_start: 0.8129 (m-30) cc_final: 0.7929 (t0) REVERT: A 962 GLU cc_start: 0.8121 (tp30) cc_final: 0.7795 (tp30) REVERT: A 1015 GLN cc_start: 0.8057 (mm110) cc_final: 0.7832 (mm-40) REVERT: A 1078 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 1259 LEU cc_start: 0.8135 (tt) cc_final: 0.7544 (mp) outliers start: 26 outliers final: 18 residues processed: 155 average time/residue: 0.0901 time to fit residues: 20.6898 Evaluate side-chains 149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1321 MET Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 59 optimal weight: 0.0170 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 chunk 120 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 2.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094904 restraints weight = 20851.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098112 restraints weight = 11173.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100098 restraints weight = 7831.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101358 restraints weight = 6438.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101976 restraints weight = 5733.845| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11836 Z= 0.134 Angle : 0.589 12.398 16348 Z= 0.312 Chirality : 0.042 0.245 1812 Planarity : 0.003 0.034 1833 Dihedral : 20.118 177.256 2175 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.16 % Allowed : 13.21 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1238 helix: 1.77 (0.20), residues: 684 sheet: -0.58 (0.45), residues: 124 loop : -0.39 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.027 0.001 TYR B 161 PHE 0.014 0.001 PHE A1350 TRP 0.023 0.001 TRP A 908 HIS 0.004 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11835) covalent geometry : angle 0.58875 / 0.31 (16348) hydrogen bonds : bond 0.03949 / 2.51 ( 595) hydrogen bonds : angle 4.13367 / 2.82 ( 1642) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5630 (OUTLIER) cc_final: 0.5236 (tt0) REVERT: B 128 ILE cc_start: 0.7109 (mm) cc_final: 0.6836 (mp) REVERT: B 141 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 209 ASP cc_start: 0.8225 (t0) cc_final: 0.7891 (t0) REVERT: B 329 MET cc_start: 0.7570 (tpp) cc_final: 0.7184 (tpp) REVERT: A 533 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8447 (ttp-170) REVERT: A 796 ASP cc_start: 0.8217 (m-30) cc_final: 0.7909 (m-30) REVERT: A 905 ASP cc_start: 0.8111 (m-30) cc_final: 0.7903 (t0) REVERT: A 962 GLU cc_start: 0.8075 (tp30) cc_final: 0.7745 (tp30) REVERT: A 1078 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 1176 GLU cc_start: 0.8551 (tp30) cc_final: 0.8297 (tp30) REVERT: A 1259 LEU cc_start: 0.8151 (tt) cc_final: 0.7550 (mp) REVERT: A 1278 LEU cc_start: 0.7707 (mp) cc_final: 0.7404 (tp) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.0792 time to fit residues: 17.9063 Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 0.0070 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094668 restraints weight = 20749.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097743 restraints weight = 11288.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099711 restraints weight = 8019.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100814 restraints weight = 6574.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101577 restraints weight = 5894.940| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11836 Z= 0.151 Angle : 0.593 9.743 16348 Z= 0.318 Chirality : 0.042 0.260 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.037 172.303 2175 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.34 % Allowed : 13.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1238 helix: 1.77 (0.20), residues: 685 sheet: -0.45 (0.46), residues: 120 loop : -0.49 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.013 0.001 TYR A 496 PHE 0.013 0.001 PHE A1350 TRP 0.024 0.001 TRP A 908 HIS 0.015 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (11835) covalent geometry : angle 0.59286 / 0.32 (16348) hydrogen bonds : bond 0.04025 / 2.56 ( 595) hydrogen bonds : angle 4.16285 / 2.84 ( 1642) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5603 (OUTLIER) cc_final: 0.5323 (tt0) REVERT: B 128 ILE cc_start: 0.7136 (mm) cc_final: 0.6857 (mp) REVERT: B 141 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 209 ASP cc_start: 0.8229 (t0) cc_final: 0.7887 (t0) REVERT: B 329 MET cc_start: 0.7588 (tpp) cc_final: 0.7209 (tpp) REVERT: A 533 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8445 (ttp-170) REVERT: A 796 ASP cc_start: 0.8204 (m-30) cc_final: 0.7892 (m-30) REVERT: A 962 GLU cc_start: 0.8056 (tp30) cc_final: 0.7725 (tp30) REVERT: A 1078 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 1176 GLU cc_start: 0.8583 (tp30) cc_final: 0.8344 (tp30) REVERT: A 1259 LEU cc_start: 0.8126 (tt) cc_final: 0.7500 (mp) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.0892 time to fit residues: 19.4622 Evaluate side-chains 154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 925 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096124 restraints weight = 20605.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099230 restraints weight = 11020.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101237 restraints weight = 7770.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102486 restraints weight = 6349.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103144 restraints weight = 5642.582| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11836 Z= 0.132 Angle : 0.601 15.798 16348 Z= 0.316 Chirality : 0.042 0.287 1812 Planarity : 0.003 0.035 1833 Dihedral : 19.680 144.371 2175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.69 % Allowed : 14.34 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1238 helix: 1.84 (0.20), residues: 685 sheet: -0.34 (0.47), residues: 116 loop : -0.50 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.015 0.001 TYR A 496 PHE 0.016 0.001 PHE A1350 TRP 0.030 0.001 TRP A 908 HIS 0.010 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (11835) covalent geometry : angle 0.60077 / 0.32 (16348) hydrogen bonds : bond 0.03818 / 2.45 ( 595) hydrogen bonds : angle 4.07767 / 2.78 ( 1642) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5619 (tt0) cc_final: 0.5344 (tt0) REVERT: B 128 ILE cc_start: 0.7040 (mm) cc_final: 0.6750 (mp) REVERT: B 141 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 209 ASP cc_start: 0.8169 (t0) cc_final: 0.7824 (t0) REVERT: B 329 MET cc_start: 0.7571 (tpp) cc_final: 0.7188 (tpp) REVERT: A 533 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8367 (ttp-170) REVERT: A 796 ASP cc_start: 0.8166 (m-30) cc_final: 0.7835 (m-30) REVERT: A 962 GLU cc_start: 0.8058 (tp30) cc_final: 0.7726 (tp30) REVERT: A 1078 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 1176 GLU cc_start: 0.8569 (tp30) cc_final: 0.8357 (tp30) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.0859 time to fit residues: 19.6508 Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 126 optimal weight: 50.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 925 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095562 restraints weight = 20505.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098688 restraints weight = 11057.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100670 restraints weight = 7787.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101754 restraints weight = 6379.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102540 restraints weight = 5728.875| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11836 Z= 0.143 Angle : 0.609 13.529 16348 Z= 0.320 Chirality : 0.042 0.297 1812 Planarity : 0.003 0.034 1833 Dihedral : 19.422 145.183 2175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 14.62 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1238 helix: 1.82 (0.20), residues: 685 sheet: -0.32 (0.47), residues: 116 loop : -0.50 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.026 0.001 TYR B 161 PHE 0.014 0.001 PHE A 826 TRP 0.028 0.001 TRP A 908 HIS 0.009 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (11835) covalent geometry : angle 0.60925 / 0.32 (16348) hydrogen bonds : bond 0.03873 / 2.49 ( 595) hydrogen bonds : angle 4.08777 / 2.79 ( 1642) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5595 (tt0) cc_final: 0.5329 (tt0) REVERT: B 128 ILE cc_start: 0.7052 (mm) cc_final: 0.6766 (mp) REVERT: B 141 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7260 (tm-30) REVERT: B 209 ASP cc_start: 0.8157 (t0) cc_final: 0.7807 (t0) REVERT: B 329 MET cc_start: 0.7568 (tpp) cc_final: 0.7187 (tpp) REVERT: A 533 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8359 (ttp-170) REVERT: A 796 ASP cc_start: 0.8167 (m-30) cc_final: 0.7842 (m-30) REVERT: A 856 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7974 (mmmm) REVERT: A 962 GLU cc_start: 0.8056 (tp30) cc_final: 0.7736 (tp30) REVERT: A 1078 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 1176 GLU cc_start: 0.8550 (tp30) cc_final: 0.8342 (tp30) REVERT: A 1259 LEU cc_start: 0.8012 (tt) cc_final: 0.7392 (mp) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 0.0870 time to fit residues: 19.1238 Evaluate side-chains 152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 925 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096868 restraints weight = 20642.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100024 restraints weight = 11024.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102032 restraints weight = 7734.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103251 restraints weight = 6322.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103874 restraints weight = 5627.033| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11836 Z= 0.126 Angle : 0.611 13.610 16348 Z= 0.320 Chirality : 0.042 0.309 1812 Planarity : 0.003 0.035 1833 Dihedral : 19.271 146.524 2175 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.69 % Allowed : 14.90 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.24), residues: 1238 helix: 1.86 (0.20), residues: 684 sheet: -0.26 (0.47), residues: 116 loop : -0.51 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.013 0.001 TYR A 496 PHE 0.016 0.001 PHE A1350 TRP 0.030 0.001 TRP A 908 HIS 0.008 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (11835) covalent geometry : angle 0.61067 / 0.32 (16348) hydrogen bonds : bond 0.03756 / 2.43 ( 595) hydrogen bonds : angle 4.03277 / 2.75 ( 1642) Misc. bond : bond 0.00079 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.5487 (tt0) cc_final: 0.5232 (tt0) REVERT: B 128 ILE cc_start: 0.7024 (mm) cc_final: 0.6729 (mp) REVERT: B 209 ASP cc_start: 0.8101 (t0) cc_final: 0.7762 (t0) REVERT: B 329 MET cc_start: 0.7560 (tpp) cc_final: 0.7174 (tpp) REVERT: A 533 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8354 (ttp-170) REVERT: A 796 ASP cc_start: 0.8151 (m-30) cc_final: 0.7832 (m-30) REVERT: A 856 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7970 (mmmm) REVERT: A 962 GLU cc_start: 0.8048 (tp30) cc_final: 0.7729 (tp30) REVERT: A 1078 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 1259 LEU cc_start: 0.8030 (tt) cc_final: 0.7456 (mt) outliers start: 18 outliers final: 16 residues processed: 152 average time/residue: 0.0855 time to fit residues: 18.9206 Evaluate side-chains 154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095857 restraints weight = 20789.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098966 restraints weight = 11254.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100956 restraints weight = 7954.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102201 restraints weight = 6511.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102917 restraints weight = 5803.801| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11836 Z= 0.144 Angle : 0.615 13.223 16348 Z= 0.321 Chirality : 0.042 0.314 1812 Planarity : 0.003 0.034 1833 Dihedral : 19.232 147.362 2175 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.69 % Allowed : 15.00 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1238 helix: 1.80 (0.20), residues: 685 sheet: -0.30 (0.47), residues: 116 loop : -0.53 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 533 TYR 0.012 0.001 TYR A 496 PHE 0.023 0.001 PHE A1350 TRP 0.029 0.001 TRP A 908 HIS 0.008 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (11835) covalent geometry : angle 0.61464 / 0.32 (16348) hydrogen bonds : bond 0.03832 / 2.50 ( 595) hydrogen bonds : angle 4.06425 / 2.77 ( 1642) Misc. bond : bond 0.00071 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.61 seconds wall clock time: 28 minutes 33.76 seconds (1713.76 seconds total)