Starting phenix.real_space_refine on Fri Jul 3 01:28:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5u_16443/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5u_16443/07_2026/8c5u_16443.cif" } 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-dev-6108/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: {'RNA': 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: 2.55, per 1000 atoms: 0.22 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: 0.90 Conformation dependent library (CDL) restraints added in 549.5 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: 1.22 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: 2.72 Time building geometry restraints manager: 1.17 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=" 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=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 1.607 1.704 -0.097 1.50e-02 4.44e+03 4.21e+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=" C3' DA T 19 " pdb=" C2' DA T 19 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.05e+01 ... (remaining 11830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16178 3.01 - 6.01: 151 6.01 - 9.02: 13 9.02 - 12.02: 4 12.02 - 15.03: 2 Bond angle restraints: 16348 Sorted by residual: 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=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 120.20 112.88 7.32 1.50e+00 4.44e-01 2.38e+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: 6477 29.60 - 59.19: 439 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=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 24.00 -30.76 54.76 1 8.00e+00 1.56e-02 6.35e+01 dihedral pdb=" C5' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" O3' G C 108 " ideal model delta sinusoidal sigma weight residual 147.00 93.88 53.12 1 8.00e+00 1.56e-02 6.00e+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 -35.00 13.18 -48.18 1 8.00e+00 1.56e-02 5.00e+01 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1737 0.107 - 0.213: 65 0.213 - 0.320: 7 0.320 - 0.426: 1 0.426 - 0.533: 2 Chirality restraints: 1812 Sorted by residual: 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 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 2.41 2.81 -0.40 2.00e-01 2.50e+01 3.97e+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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- 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= 0.298 Angle : 0.742 15.031 16348 Z= 0.434 Chirality : 0.053 0.533 1812 Planarity : 0.004 0.034 1833 Dihedral : 18.254 147.972 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 / 0.29 (11835) covalent geometry : angle 0.74216 / 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 : 0.395 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: 0.0991 time to fit residues: 25.0514 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 : 0.369 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.127799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094672 restraints weight = 20894.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097701 restraints weight = 11267.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099680 restraints weight = 7975.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100732 restraints weight = 6524.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101565 restraints weight = 5848.957| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11836 Z= 0.197 Angle : 0.644 9.354 16348 Z= 0.351 Chirality : 0.044 0.181 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.209 151.516 2175 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.50 % Allowed : 8.15 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.73 (0.20), residues: 676 sheet: -0.61 (0.45), residues: 128 loop : -0.42 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1151 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 A 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (11835) covalent geometry : angle 0.64355 / 0.35 (16348) hydrogen bonds : bond 0.05016 / 3.19 ( 595) hydrogen bonds : angle 4.49687 / 3.05 ( 1642) Misc. bond : bond 0.00223 / 0.12 ( 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 162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 131 LYS cc_start: 0.8271 (mptt) cc_final: 0.8031 (mppt) REVERT: B 209 ASP cc_start: 0.8296 (t0) cc_final: 0.8008 (t0) REVERT: B 329 MET cc_start: 0.7554 (tpp) cc_final: 0.7093 (tpp) REVERT: A 533 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8203 (ttp-170) REVERT: A 796 ASP cc_start: 0.8178 (m-30) cc_final: 0.7873 (m-30) REVERT: A 905 ASP cc_start: 0.8158 (m-30) cc_final: 0.7896 (t0) REVERT: A 962 GLU cc_start: 0.8046 (tp30) cc_final: 0.7712 (tp30) REVERT: A 1078 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 1197 ASP cc_start: 0.8388 (m-30) cc_final: 0.8183 (m-30) REVERT: A 1259 LEU cc_start: 0.8227 (tt) cc_final: 0.7683 (mt) outliers start: 16 outliers final: 11 residues processed: 156 average time/residue: 0.1012 time to fit residues: 22.8128 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 533 ARG 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: 4.9990 chunk 75 optimal weight: 0.7980 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: 9.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 GLN B 308 ASN A1036 GLN 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 = 0.3675 r_free = 0.3675 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093712 restraints weight = 21152.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096773 restraints weight = 11524.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098728 restraints weight = 8174.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099955 restraints weight = 6714.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100501 restraints weight = 5976.424| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11836 Z= 0.176 Angle : 0.594 8.592 16348 Z= 0.325 Chirality : 0.042 0.174 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.196 156.926 2175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.97 % Allowed : 9.65 % Favored : 88.38 % 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: 1.04 (0.24), residues: 1238 helix: 1.73 (0.20), residues: 678 sheet: -0.62 (0.45), residues: 128 loop : -0.50 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 533 TYR 0.025 0.001 TYR A 496 PHE 0.022 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 0.00378 / 0.18 (11835) covalent geometry : angle 0.59401 / 0.32 (16348) hydrogen bonds : bond 0.04481 / 2.87 ( 595) hydrogen bonds : angle 4.34390 / 2.95 ( 1642) Misc. bond : bond 0.00000 / 0.00 ( 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 : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 209 ASP cc_start: 0.8230 (t0) cc_final: 0.7931 (t0) REVERT: B 329 MET cc_start: 0.7620 (tpp) cc_final: 0.7269 (tpp) REVERT: A 796 ASP cc_start: 0.8218 (m-30) cc_final: 0.7928 (m-30) REVERT: A 905 ASP cc_start: 0.8114 (m-30) cc_final: 0.7898 (t0) REVERT: A 962 GLU cc_start: 0.8042 (tp30) cc_final: 0.7726 (tp30) REVERT: A 1015 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7805 (mm-40) REVERT: A 1078 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 1259 LEU cc_start: 0.8168 (tt) cc_final: 0.7568 (mp) outliers start: 21 outliers final: 15 residues processed: 152 average time/residue: 0.0959 time to fit residues: 21.1991 Evaluate side-chains 142 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 126 optimal weight: 50.0000 chunk 82 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091797 restraints weight = 21048.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094782 restraints weight = 11575.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096686 restraints weight = 8261.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097815 restraints weight = 6806.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098412 restraints weight = 6105.555| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11836 Z= 0.238 Angle : 0.640 12.667 16348 Z= 0.345 Chirality : 0.044 0.202 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.225 162.513 2175 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 12.00 % Favored : 85.38 % 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: 0.80 (0.23), residues: 1238 helix: 1.51 (0.19), residues: 680 sheet: -0.71 (0.45), residues: 124 loop : -0.59 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 533 TYR 0.025 0.002 TYR B 161 PHE 0.017 0.001 PHE A1350 TRP 0.021 0.002 TRP A 908 HIS 0.005 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (11835) covalent geometry : angle 0.64026 / 0.34 (16348) hydrogen bonds : bond 0.04638 / 2.94 ( 595) hydrogen bonds : angle 4.47272 / 3.06 ( 1642) Misc. bond : bond 0.00011 / 0.01 ( 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 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 209 ASP cc_start: 0.8291 (t0) cc_final: 0.7991 (t0) REVERT: B 329 MET cc_start: 0.7656 (tpp) cc_final: 0.7291 (tpp) REVERT: A 796 ASP cc_start: 0.8233 (m-30) cc_final: 0.7877 (m-30) REVERT: A 905 ASP cc_start: 0.8145 (m-30) cc_final: 0.7914 (t0) REVERT: A 962 GLU cc_start: 0.8154 (tp30) cc_final: 0.7840 (tp30) REVERT: A 1078 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 1259 LEU cc_start: 0.8115 (tt) cc_final: 0.7576 (mp) REVERT: A 1278 LEU cc_start: 0.7804 (mp) cc_final: 0.7474 (tp) outliers start: 28 outliers final: 16 residues processed: 150 average time/residue: 0.0920 time to fit residues: 20.3153 Evaluate side-chains 147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 218 SER 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 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 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: 9.9990 chunk 47 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3663 r_free = 0.3663 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.092610 restraints weight = 20911.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095596 restraints weight = 11368.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097542 restraints weight = 8092.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098742 restraints weight = 6634.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099370 restraints weight = 5917.916| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1688 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= 0.186 Angle : 0.597 8.135 16348 Z= 0.325 Chirality : 0.042 0.218 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.179 170.195 2175 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 2.62 % Allowed : 12.65 % Favored : 84.72 % 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: 0.84 (0.24), residues: 1238 helix: 1.54 (0.20), residues: 682 sheet: -0.65 (0.47), residues: 116 loop : -0.60 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.014 0.001 TYR A 496 PHE 0.016 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 0.00408 / 0.19 (11835) covalent geometry : angle 0.59704 / 0.32 (16348) hydrogen bonds : bond 0.04341 / 2.76 ( 595) hydrogen bonds : angle 4.34800 / 2.96 ( 1642) Misc. bond : bond 0.00013 / 0.01 ( 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 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 209 ASP cc_start: 0.8337 (t0) cc_final: 0.7998 (t0) REVERT: B 329 MET cc_start: 0.7645 (tpp) cc_final: 0.7284 (tpp) REVERT: A 533 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8310 (ttp-170) REVERT: A 796 ASP cc_start: 0.8196 (m-30) cc_final: 0.7825 (m-30) REVERT: A 962 GLU cc_start: 0.8137 (tp30) cc_final: 0.7823 (tp30) REVERT: A 1259 LEU cc_start: 0.8123 (tt) cc_final: 0.7529 (mp) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.0953 time to fit residues: 20.6533 Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 489 VAL 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 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 1137 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: 7.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 120 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.127826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094127 restraints weight = 20804.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097220 restraints weight = 11255.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099151 restraints weight = 7961.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100356 restraints weight = 6551.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100905 restraints weight = 5842.946| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11836 Z= 0.140 Angle : 0.587 12.183 16348 Z= 0.315 Chirality : 0.041 0.235 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.120 177.324 2175 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.60 % 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: 0.94 (0.24), residues: 1238 helix: 1.65 (0.20), residues: 682 sheet: -0.54 (0.45), residues: 122 loop : -0.64 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.013 0.001 TYR A 496 PHE 0.014 0.001 PHE A1350 TRP 0.024 0.001 TRP A 908 HIS 0.003 0.001 HIS A 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11835) covalent geometry : angle 0.58721 / 0.32 (16348) hydrogen bonds : bond 0.04099 / 2.61 ( 595) hydrogen bonds : angle 4.22804 / 2.89 ( 1642) Misc. bond : bond 0.00066 / 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 160 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 209 ASP cc_start: 0.8279 (t0) cc_final: 0.7936 (t0) REVERT: B 329 MET cc_start: 0.7621 (tpp) cc_final: 0.7263 (tpp) REVERT: A 533 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8321 (ttp-170) REVERT: A 796 ASP cc_start: 0.8229 (m-30) cc_final: 0.7854 (m-30) REVERT: A 962 GLU cc_start: 0.8101 (tp30) cc_final: 0.7788 (tp30) REVERT: A 1078 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6867 (tm-30) REVERT: A 1176 GLU cc_start: 0.8529 (tp30) cc_final: 0.8314 (tp30) REVERT: A 1259 LEU cc_start: 0.8157 (tt) cc_final: 0.7552 (mp) REVERT: A 1278 LEU cc_start: 0.7689 (mp) cc_final: 0.7362 (tp) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 0.0955 time to fit residues: 21.1210 Evaluate side-chains 152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3662 r_free = 0.3662 target = 0.126228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.092656 restraints weight = 20839.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095638 restraints weight = 11386.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097540 restraints weight = 8128.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098702 restraints weight = 6697.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099323 restraints weight = 5993.422| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11836 Z= 0.200 Angle : 0.623 9.495 16348 Z= 0.334 Chirality : 0.043 0.248 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.107 174.430 2175 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.44 % Allowed : 14.90 % Favored : 82.66 % 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: 0.88 (0.23), residues: 1238 helix: 1.56 (0.20), residues: 684 sheet: -0.46 (0.48), residues: 108 loop : -0.64 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.027 0.001 TYR B 161 PHE 0.014 0.001 PHE A 826 TRP 0.024 0.001 TRP A 908 HIS 0.004 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (11835) covalent geometry : angle 0.62273 / 0.33 (16348) hydrogen bonds : bond 0.04383 / 2.79 ( 595) hydrogen bonds : angle 4.32440 / 2.95 ( 1642) Misc. bond : bond 0.00018 / 0.01 ( 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 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LEU cc_start: 0.7704 (tp) cc_final: 0.7453 (tp) REVERT: B 141 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 329 MET cc_start: 0.7636 (tpp) cc_final: 0.7283 (tpp) REVERT: A 796 ASP cc_start: 0.8207 (m-30) cc_final: 0.7833 (m-30) REVERT: A 962 GLU cc_start: 0.8117 (tp30) cc_final: 0.7807 (tp30) REVERT: A 1176 GLU cc_start: 0.8560 (tp30) cc_final: 0.8331 (tp30) REVERT: A 1259 LEU cc_start: 0.8144 (tt) cc_final: 0.7516 (mp) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.0802 time to fit residues: 16.9385 Evaluate side-chains 141 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 665 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 1296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095185 restraints weight = 20648.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098258 restraints weight = 11164.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100215 restraints weight = 7917.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101379 restraints weight = 6501.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102184 restraints weight = 5804.127| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1914 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= 0.130 Angle : 0.605 14.771 16348 Z= 0.322 Chirality : 0.041 0.265 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.887 160.294 2175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.50 % Allowed : 16.31 % Favored : 82.19 % 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: 1.02 (0.24), residues: 1238 helix: 1.68 (0.20), residues: 684 sheet: -0.36 (0.47), residues: 116 loop : -0.59 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.014 0.001 TYR A 496 PHE 0.019 0.001 PHE A1350 TRP 0.027 0.001 TRP A 908 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (11835) covalent geometry : angle 0.60489 / 0.32 (16348) hydrogen bonds : bond 0.04005 / 2.57 ( 595) hydrogen bonds : angle 4.17227 / 2.85 ( 1642) Misc. bond : bond 0.00029 / 0.02 ( 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 160 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 209 ASP cc_start: 0.8254 (t0) cc_final: 0.7887 (t0) REVERT: B 329 MET cc_start: 0.7562 (tpp) cc_final: 0.7208 (tpp) REVERT: A 533 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8270 (ttp-170) REVERT: A 796 ASP cc_start: 0.8203 (m-30) cc_final: 0.7863 (m-30) REVERT: A 856 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7971 (mmmm) REVERT: A 962 GLU cc_start: 0.8111 (tp30) cc_final: 0.7804 (tp30) REVERT: A 1078 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6802 (tm-30) REVERT: A 1176 GLU cc_start: 0.8548 (tp30) cc_final: 0.8299 (tp30) REVERT: A 1259 LEU cc_start: 0.8134 (tt) cc_final: 0.7504 (mp) outliers start: 16 outliers final: 14 residues processed: 155 average time/residue: 0.0879 time to fit residues: 19.8441 Evaluate side-chains 149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 51 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.0030 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 126 optimal weight: 50.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** 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 = 0.3682 r_free = 0.3682 target = 0.127765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094440 restraints weight = 20632.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097491 restraints weight = 11207.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099420 restraints weight = 7929.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100632 restraints weight = 6520.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101208 restraints weight = 5814.341| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11836 Z= 0.151 Angle : 0.615 13.776 16348 Z= 0.325 Chirality : 0.042 0.275 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.662 146.084 2175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 15.75 % Favored : 82.47 % 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: 1.02 (0.24), residues: 1238 helix: 1.67 (0.20), residues: 685 sheet: -0.37 (0.47), residues: 116 loop : -0.58 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.013 0.001 TYR A 496 PHE 0.018 0.001 PHE A1350 TRP 0.028 0.001 TRP A 908 HIS 0.019 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11835) covalent geometry : angle 0.61456 / 0.32 (16348) hydrogen bonds : bond 0.04064 / 2.61 ( 595) hydrogen bonds : angle 4.18084 / 2.85 ( 1642) Misc. bond : bond 0.00036 / 0.02 ( 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 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.7088 (mm) cc_final: 0.6802 (mp) REVERT: B 141 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 329 MET cc_start: 0.7584 (tpp) cc_final: 0.7227 (tpp) REVERT: A 533 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8274 (ttp-170) REVERT: A 796 ASP cc_start: 0.8216 (m-30) cc_final: 0.7856 (m-30) REVERT: A 856 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7970 (mmmm) REVERT: A 962 GLU cc_start: 0.8113 (tp30) cc_final: 0.7814 (tp30) REVERT: A 1078 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 1176 GLU cc_start: 0.8548 (tp30) cc_final: 0.8323 (tp30) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.0881 time to fit residues: 19.0200 Evaluate side-chains 151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.129557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096253 restraints weight = 20669.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099328 restraints weight = 11115.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101346 restraints weight = 7853.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102513 restraints weight = 6426.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103257 restraints weight = 5731.154| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11836 Z= 0.126 Angle : 0.615 13.554 16348 Z= 0.322 Chirality : 0.041 0.291 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.254 148.349 2175 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 16.59 % Favored : 82.01 % 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: 1.10 (0.24), residues: 1238 helix: 1.75 (0.20), residues: 684 sheet: -0.31 (0.47), residues: 116 loop : -0.55 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.032 0.001 TYR B 161 PHE 0.022 0.001 PHE A1350 TRP 0.032 0.001 TRP A 908 HIS 0.014 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (11835) covalent geometry : angle 0.61493 / 0.32 (16348) hydrogen bonds : bond 0.03806 / 2.46 ( 595) hydrogen bonds : angle 4.07321 / 2.78 ( 1642) Misc. bond : bond 0.00075 / 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 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.7073 (mm) cc_final: 0.6773 (mp) REVERT: B 141 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 209 ASP cc_start: 0.8193 (t0) cc_final: 0.7813 (t0) REVERT: B 329 MET cc_start: 0.7548 (tpp) cc_final: 0.7188 (tpp) REVERT: A 533 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8304 (ttp-170) REVERT: A 796 ASP cc_start: 0.8190 (m-30) cc_final: 0.7864 (m-30) REVERT: A 856 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7965 (mmmm) REVERT: A 962 GLU cc_start: 0.8056 (tp30) cc_final: 0.7754 (tp30) REVERT: A 1078 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6755 (tm-30) REVERT: A 1259 LEU cc_start: 0.8013 (tt) cc_final: 0.7409 (mp) outliers start: 15 outliers final: 12 residues processed: 150 average time/residue: 0.0951 time to fit residues: 20.4031 Evaluate side-chains 149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 656 ILE Chi-restraints excluded: chain A residue 675 MET 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 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 125 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094933 restraints weight = 20838.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097970 restraints weight = 11287.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099942 restraints weight = 7991.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101155 restraints weight = 6537.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101774 restraints weight = 5836.204| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11836 Z= 0.158 Angle : 0.617 13.093 16348 Z= 0.325 Chirality : 0.042 0.296 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.249 149.356 2175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.59 % Allowed : 16.31 % Favored : 82.10 % 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: 1.04 (0.24), residues: 1238 helix: 1.69 (0.20), residues: 685 sheet: -0.36 (0.47), residues: 116 loop : -0.57 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 533 TYR 0.014 0.001 TYR A 496 PHE 0.028 0.001 PHE A1350 TRP 0.028 0.001 TRP A 908 HIS 0.014 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (11835) covalent geometry : angle 0.61687 / 0.33 (16348) hydrogen bonds : bond 0.03990 / 2.61 ( 595) hydrogen bonds : angle 4.13173 / 2.82 ( 1642) Misc. bond : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.01 seconds wall clock time: 30 minutes 8.35 seconds (1808.35 seconds total)