Starting phenix.real_space_refine on Fri Jul 3 07:07:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.map" model { file = "/net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jwk_61853/07_2026/9jwk_61853.cif" } resolution = 3.46 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. 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 139 5.49 5 S 35 5.16 5 C 7352 2.51 5 N 2149 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 12414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9473 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 35, 'TRANS': 1128} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2492 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 12, 'rna3p_pur': 56, 'rna3p_pyr': 42} Link IDs: {'rna2p': 19, 'rna3p': 97} Chain breaks: 2 Chain: "D" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.24 Number of scatterers: 12414 At special positions: 0 Unit cell: (95.45, 120.35, 141.93, 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 139 15.00 O 2739 8.00 N 2149 7.00 C 7352 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=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 563.5 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 51.0% alpha, 8.4% beta 46 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 57 through 92 removed outlier: 4.731A pdb=" N ASN A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.839A pdb=" N ASN A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.720A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.588A pdb=" N THR A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 218 through 231 removed outlier: 4.154A pdb=" N GLN A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 278 through 287 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 304 through 312 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.540A pdb=" N ARG A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 389 through 402 Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.372A pdb=" N PHE A 433 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 434 " --> pdb=" O ASN A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 435 through 452 removed outlier: 3.584A pdb=" N GLN A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.935A pdb=" N LEU A 457 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 518 through 531 Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.584A pdb=" N LYS A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Processing helix chain 'A' and resid 661 through 673 removed outlier: 4.275A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 750 through 754 removed outlier: 4.024A pdb=" N ILE A 754 " --> pdb=" O ILE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.953A pdb=" N GLY A 761 " --> pdb=" O ASP A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 787 Processing helix chain 'A' and resid 965 through 977 removed outlier: 4.028A pdb=" N ILE A 969 " --> pdb=" O GLY A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.983A pdb=" N THR A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1027 removed outlier: 4.389A pdb=" N ALA A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1055 Processing helix chain 'A' and resid 1068 through 1070 No H-bonds generated for 'chain 'A' and resid 1068 through 1070' Processing helix chain 'A' and resid 1071 through 1082 removed outlier: 3.628A pdb=" N PHE A1082 " --> pdb=" O LYS A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 Processing helix chain 'A' and resid 1164 through 1166 No H-bonds generated for 'chain 'A' and resid 1164 through 1166' Processing helix chain 'A' and resid 1171 through 1182 Processing helix chain 'A' and resid 1229 through 1244 Processing helix chain 'A' and resid 1252 through 1274 Processing helix chain 'A' and resid 1277 through 1282 Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1294 through 1299 removed outlier: 3.857A pdb=" N VAL A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS A1299 " --> pdb=" O GLU A1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1294 through 1299' Processing helix chain 'A' and resid 1301 through 1314 Processing helix chain 'A' and resid 1315 through 1317 No H-bonds generated for 'chain 'A' and resid 1315 through 1317' Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 4.609A pdb=" N LEU A1328 " --> pdb=" O ASP A1325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 985 removed outlier: 6.704A pdb=" N ILE A 793 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 985 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET A 795 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 792 " --> pdb=" O TYR A 15 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 796 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET A 21 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.626A pdb=" N ALA A 252 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 542 through 544 removed outlier: 5.927A pdb=" N LEU A 543 " --> pdb=" O GLY A 693 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 1058 through 1060 removed outlier: 6.992A pdb=" N ARG A1060 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A1064 " --> pdb=" O ARG A1060 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1189 through 1195 removed outlier: 6.597A pdb=" N LEU A1145 " --> pdb=" O ARG A1191 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A1193 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A1143 " --> pdb=" O THR A1193 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A1195 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N SER A1141 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A1161 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A1143 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU A1159 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A1145 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER A1157 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU A1147 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A1155 " --> pdb=" O GLU A1147 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN A1149 " --> pdb=" O LYS A1153 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS A1153 " --> pdb=" O GLN A1149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1339 through 1341 removed outlier: 3.587A pdb=" N GLY A1212 " --> pdb=" O SER A1219 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A1221 " --> pdb=" O LEU A1210 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU A1210 " --> pdb=" O SER A1221 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A1200 " --> pdb=" O ILE A1355 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3404 1.34 - 1.46: 3237 1.46 - 1.58: 5964 1.58 - 1.70: 274 1.70 - 1.82: 58 Bond restraints: 12937 Sorted by residual: bond pdb=" N ILE A 352 " pdb=" CA ILE A 352 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" CA HIS A 137 " pdb=" C HIS A 137 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.34e-02 5.57e+03 8.05e+00 bond pdb=" C3' DG D 20 " pdb=" C2' DG D 20 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.34e+00 bond pdb=" CA TYR A 136 " pdb=" C TYR A 136 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.35e-02 5.49e+03 6.89e+00 bond pdb=" C3' DC D 21 " pdb=" C2' DC D 21 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.60e+00 ... (remaining 12932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 18007 3.34 - 6.69: 79 6.69 - 10.03: 3 10.03 - 13.37: 2 13.37 - 16.72: 1 Bond angle restraints: 18092 Sorted by residual: angle pdb=" N HIS A 137 " pdb=" CA HIS A 137 " pdb=" C HIS A 137 " ideal model delta sigma weight residual 110.80 94.08 16.72 2.13e+00 2.20e-01 6.16e+01 angle pdb=" C1' C B 69 " pdb=" N1 C B 69 " pdb=" C2 C B 69 " ideal model delta sigma weight residual 118.80 124.79 -5.99 1.10e+00 8.26e-01 2.97e+01 angle pdb=" C1' U B 30 " pdb=" N1 U B 30 " pdb=" C2 U B 30 " ideal model delta sigma weight residual 117.70 123.87 -6.17 1.20e+00 6.94e-01 2.64e+01 angle pdb=" N1 U B 30 " pdb=" C2 U B 30 " pdb=" O2 U B 30 " ideal model delta sigma weight residual 122.80 126.38 -3.58 7.00e-01 2.04e+00 2.62e+01 angle pdb=" O2 C B 69 " pdb=" C2 C B 69 " pdb=" N3 C B 69 " ideal model delta sigma weight residual 121.90 118.50 3.40 7.00e-01 2.04e+00 2.36e+01 ... (remaining 18087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 7394 35.55 - 71.10: 450 71.10 - 106.65: 50 106.65 - 142.20: 1 142.20 - 177.75: 5 Dihedral angle restraints: 7900 sinusoidal: 4480 harmonic: 3420 Sorted by residual: dihedral pdb=" O4' C B 69 " pdb=" C1' C B 69 " pdb=" N1 C B 69 " pdb=" C2 C B 69 " ideal model delta sinusoidal sigma weight residual 200.00 54.28 145.72 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U B 85 " pdb=" C1' U B 85 " pdb=" N1 U B 85 " pdb=" C2 U B 85 " ideal model delta sinusoidal sigma weight residual -128.00 49.75 -177.75 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 93 " pdb=" C1' U B 93 " pdb=" N1 U B 93 " pdb=" C2 U B 93 " ideal model delta sinusoidal sigma weight residual 232.00 56.15 175.85 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1822 0.057 - 0.114: 239 0.114 - 0.172: 25 0.172 - 0.229: 3 0.229 - 0.286: 2 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA HIS A 137 " pdb=" N HIS A 137 " pdb=" C HIS A 137 " pdb=" CB HIS A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU A 138 " pdb=" CB LEU A 138 " pdb=" CD1 LEU A 138 " pdb=" CD2 LEU A 138 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TYR A 136 " pdb=" N TYR A 136 " pdb=" C TYR A 136 " pdb=" CB TYR A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2088 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1085 " -0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A1086 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1086 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1086 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 999 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1000 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1000 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1000 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1075 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LYS A1075 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A1075 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A1076 " 0.010 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 555 2.71 - 3.25: 12166 3.25 - 3.80: 21780 3.80 - 4.35: 26887 4.35 - 4.90: 41707 Nonbonded interactions: 103095 Sorted by model distance: nonbonded pdb=" O2' C B 69 " pdb=" OP1 A B 70 " model vdw 2.157 3.040 nonbonded pdb=" O ALA A 718 " pdb=" OG1 THR A 722 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A1008 " pdb=" OE1 GLU A1225 " model vdw 2.244 3.040 nonbonded pdb=" O LEU A1104 " pdb=" O2' U B 24 " model vdw 2.252 3.040 nonbonded pdb=" O TYR A 35 " pdb=" OH TYR A1015 " model vdw 2.260 3.040 ... (remaining 103090 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12937 Z= 0.239 Angle : 0.630 16.716 18092 Z= 0.460 Chirality : 0.039 0.286 2091 Planarity : 0.004 0.049 1804 Dihedral : 20.593 177.746 5696 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.23 % Rotamer: Outliers : 0.58 % Allowed : 22.98 % Favored : 76.44 % 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: 0.13 (0.25), residues: 1154 helix: 1.23 (0.24), residues: 508 sheet: 0.27 (0.81), residues: 48 loop : -0.94 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 103 TYR 0.021 0.001 TYR A1209 PHE 0.015 0.001 PHE A 477 TRP 0.016 0.001 TRP A 46 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.24 (12937) covalent geometry : angle 0.63049 / 0.46 (18092) hydrogen bonds : bond 0.12433 / 8.35 ( 518) hydrogen bonds : angle 5.68289 / 4.07 ( 1385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 111 VAL cc_start: 0.8482 (m) cc_final: 0.8183 (p) REVERT: A 347 LEU cc_start: 0.8227 (tp) cc_final: 0.7948 (tt) REVERT: A 462 GLU cc_start: 0.7001 (tp30) cc_final: 0.6598 (tp30) REVERT: A 660 ASP cc_start: 0.7524 (t0) cc_final: 0.7149 (t0) REVERT: A 769 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7645 (mtp85) outliers start: 6 outliers final: 2 residues processed: 242 average time/residue: 0.1209 time to fit residues: 40.0937 Evaluate side-chains 235 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1309 ILE 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: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 163 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116874 restraints weight = 18430.543| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.92 r_work: 0.3163 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12937 Z= 0.151 Angle : 0.537 8.047 18092 Z= 0.310 Chirality : 0.038 0.219 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.941 178.260 3290 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.31 % Allowed : 21.73 % Favored : 75.96 % 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: 0.16 (0.25), residues: 1154 helix: 1.18 (0.23), residues: 530 sheet: 0.09 (0.83), residues: 48 loop : -0.92 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.017 0.001 TYR A1209 PHE 0.008 0.001 PHE A 699 TRP 0.016 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (12937) covalent geometry : angle 0.53681 / 0.31 (18092) hydrogen bonds : bond 0.05130 / 3.50 ( 518) hydrogen bonds : angle 4.60260 / 3.28 ( 1385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.246 Fit side-chains REVERT: A 19 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 34 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 163 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: A 410 LYS cc_start: 0.8149 (tttm) cc_final: 0.7921 (tttm) REVERT: A 660 ASP cc_start: 0.8199 (t0) cc_final: 0.7845 (t0) REVERT: A 769 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8104 (mtp85) REVERT: A 1152 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7468 (mtmm) outliers start: 24 outliers final: 14 residues processed: 243 average time/residue: 0.1147 time to fit residues: 38.4108 Evaluate side-chains 245 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113432 restraints weight = 18620.608| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.94 r_work: 0.3176 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12937 Z= 0.275 Angle : 0.593 8.862 18092 Z= 0.336 Chirality : 0.042 0.233 2091 Planarity : 0.004 0.044 1804 Dihedral : 19.911 179.760 3288 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.46 % Allowed : 21.44 % Favored : 75.10 % 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: -0.11 (0.25), residues: 1154 helix: 0.92 (0.23), residues: 538 sheet: 0.21 (0.85), residues: 38 loop : -1.06 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 103 TYR 0.024 0.002 TYR A 377 PHE 0.013 0.002 PHE A1144 TRP 0.020 0.002 TRP A 46 HIS 0.008 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (12937) covalent geometry : angle 0.59287 / 0.34 (18092) hydrogen bonds : bond 0.05236 / 3.50 ( 518) hydrogen bonds : angle 4.54736 / 3.23 ( 1385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 34 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 462 GLU cc_start: 0.7675 (tp30) cc_final: 0.7124 (tp30) REVERT: A 660 ASP cc_start: 0.8269 (t0) cc_final: 0.7929 (t0) REVERT: A 755 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 769 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8170 (mtp85) REVERT: A 1152 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7547 (mtmm) outliers start: 36 outliers final: 24 residues processed: 263 average time/residue: 0.1299 time to fit residues: 46.8096 Evaluate side-chains 262 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1339 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 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 = 0.3731 r_free = 0.3731 target = 0.142595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115002 restraints weight = 18483.080| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.91 r_work: 0.3206 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12937 Z= 0.162 Angle : 0.544 8.190 18092 Z= 0.311 Chirality : 0.039 0.223 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.940 179.317 3288 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.56 % Allowed : 21.92 % Favored : 74.52 % 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: 0.04 (0.25), residues: 1154 helix: 1.16 (0.23), residues: 531 sheet: 0.08 (0.81), residues: 44 loop : -1.06 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 749 TYR 0.024 0.001 TYR A 351 PHE 0.008 0.001 PHE A 95 TRP 0.013 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (12937) covalent geometry : angle 0.54432 / 0.31 (18092) hydrogen bonds : bond 0.04698 / 3.15 ( 518) hydrogen bonds : angle 4.41409 / 3.13 ( 1385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 34 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 136 TYR cc_start: 0.7966 (m-80) cc_final: 0.7647 (m-80) REVERT: A 462 GLU cc_start: 0.7733 (tp30) cc_final: 0.7167 (tp30) REVERT: A 660 ASP cc_start: 0.8198 (t0) cc_final: 0.7864 (t0) REVERT: A 691 GLU cc_start: 0.7513 (pm20) cc_final: 0.7262 (pm20) REVERT: A 755 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 1088 VAL cc_start: 0.8235 (t) cc_final: 0.7795 (m) REVERT: A 1152 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7555 (mtmm) outliers start: 37 outliers final: 25 residues processed: 259 average time/residue: 0.1265 time to fit residues: 45.4309 Evaluate side-chains 259 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 0.0570 chunk 99 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 104 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116234 restraints weight = 18647.598| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.90 r_work: 0.3208 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12937 Z= 0.138 Angle : 0.522 9.572 18092 Z= 0.299 Chirality : 0.038 0.218 2091 Planarity : 0.004 0.052 1804 Dihedral : 19.920 178.684 3288 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.37 % Allowed : 22.98 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1154 helix: 1.24 (0.23), residues: 535 sheet: 0.14 (0.82), residues: 43 loop : -1.02 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.017 0.001 TYR A1209 PHE 0.009 0.001 PHE A 456 TRP 0.011 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (12937) covalent geometry : angle 0.52228 / 0.30 (18092) hydrogen bonds : bond 0.04398 / 2.97 ( 518) hydrogen bonds : angle 4.29350 / 3.04 ( 1385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 34 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7838 (mm-30) REVERT: A 83 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7616 (mm-30) REVERT: A 136 TYR cc_start: 0.7975 (m-80) cc_final: 0.7639 (m-80) REVERT: A 462 GLU cc_start: 0.7734 (tp30) cc_final: 0.7154 (tp30) REVERT: A 522 SER cc_start: 0.8010 (t) cc_final: 0.7663 (m) REVERT: A 573 GLN cc_start: 0.6724 (pp30) cc_final: 0.6302 (pp30) REVERT: A 633 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 660 ASP cc_start: 0.8184 (t0) cc_final: 0.7872 (t0) REVERT: A 691 GLU cc_start: 0.7518 (pm20) cc_final: 0.7239 (pm20) REVERT: A 755 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 769 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8126 (mtp85) REVERT: A 1088 VAL cc_start: 0.8186 (t) cc_final: 0.7852 (m) REVERT: A 1152 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7556 (mtmm) outliers start: 35 outliers final: 24 residues processed: 259 average time/residue: 0.1266 time to fit residues: 45.4663 Evaluate side-chains 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 0.3980 chunk 104 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116689 restraints weight = 18478.043| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.89 r_work: 0.3198 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12937 Z= 0.137 Angle : 0.515 8.213 18092 Z= 0.294 Chirality : 0.037 0.217 2091 Planarity : 0.004 0.051 1804 Dihedral : 19.886 178.467 3288 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.65 % Allowed : 23.65 % Favored : 72.69 % 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: 0.19 (0.25), residues: 1154 helix: 1.27 (0.23), residues: 542 sheet: -0.10 (0.76), residues: 50 loop : -1.00 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.013 0.001 TYR A 377 PHE 0.011 0.001 PHE A 477 TRP 0.011 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (12937) covalent geometry : angle 0.51501 / 0.29 (18092) hydrogen bonds : bond 0.04264 / 2.88 ( 518) hydrogen bonds : angle 4.21167 / 2.99 ( 1385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 34 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 83 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7607 (mm-30) REVERT: A 136 TYR cc_start: 0.7956 (m-80) cc_final: 0.7706 (m-80) REVERT: A 163 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: A 462 GLU cc_start: 0.7707 (tp30) cc_final: 0.7128 (tp30) REVERT: A 573 GLN cc_start: 0.6747 (pp30) cc_final: 0.6313 (pp30) REVERT: A 633 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 660 ASP cc_start: 0.8191 (t0) cc_final: 0.7854 (t0) REVERT: A 691 GLU cc_start: 0.7508 (pm20) cc_final: 0.7226 (pm20) REVERT: A 755 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 1088 VAL cc_start: 0.8192 (t) cc_final: 0.7850 (m) REVERT: A 1152 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7567 (mtmm) outliers start: 38 outliers final: 26 residues processed: 254 average time/residue: 0.1224 time to fit residues: 43.0900 Evaluate side-chains 264 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1339 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116610 restraints weight = 18471.158| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.90 r_work: 0.3214 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12937 Z= 0.146 Angle : 0.517 10.673 18092 Z= 0.294 Chirality : 0.037 0.216 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.850 178.476 3288 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.37 % Allowed : 23.65 % Favored : 72.98 % 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: 0.25 (0.25), residues: 1154 helix: 1.34 (0.23), residues: 541 sheet: -0.17 (0.76), residues: 50 loop : -0.98 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.014 0.001 TYR A 377 PHE 0.008 0.001 PHE A 456 TRP 0.011 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (12937) covalent geometry : angle 0.51675 / 0.29 (18092) hydrogen bonds : bond 0.04212 / 2.84 ( 518) hydrogen bonds : angle 4.17143 / 2.96 ( 1385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 25 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 39 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7659 (ptm-80) REVERT: A 83 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7607 (mm-30) REVERT: A 136 TYR cc_start: 0.7979 (m-80) cc_final: 0.7692 (m-80) REVERT: A 163 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: A 462 GLU cc_start: 0.7664 (tp30) cc_final: 0.7104 (tp30) REVERT: A 573 GLN cc_start: 0.6744 (pp30) cc_final: 0.6261 (pp30) REVERT: A 660 ASP cc_start: 0.8192 (t0) cc_final: 0.7858 (t0) REVERT: A 691 GLU cc_start: 0.7482 (pm20) cc_final: 0.7215 (pm20) REVERT: A 720 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.8021 (ttm110) REVERT: A 727 MET cc_start: 0.7712 (mmm) cc_final: 0.7470 (mmm) REVERT: A 755 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 769 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8145 (mtp85) REVERT: A 1088 VAL cc_start: 0.8212 (t) cc_final: 0.7856 (m) REVERT: A 1152 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7564 (mtmm) REVERT: A 1209 TYR cc_start: 0.7956 (m-10) cc_final: 0.7690 (m-10) outliers start: 35 outliers final: 28 residues processed: 254 average time/residue: 0.1271 time to fit residues: 44.6241 Evaluate side-chains 262 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1339 SER Chi-restraints excluded: chain A residue 1340 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115492 restraints weight = 18526.268| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.89 r_work: 0.3213 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12937 Z= 0.189 Angle : 0.545 9.360 18092 Z= 0.309 Chirality : 0.039 0.215 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.818 179.123 3288 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.37 % Allowed : 24.33 % Favored : 72.31 % 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: 0.18 (0.25), residues: 1154 helix: 1.30 (0.23), residues: 542 sheet: -0.26 (0.75), residues: 50 loop : -1.05 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.027 0.002 TYR A 351 PHE 0.015 0.001 PHE A 477 TRP 0.014 0.001 TRP A 46 HIS 0.010 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (12937) covalent geometry : angle 0.54481 / 0.31 (18092) hydrogen bonds : bond 0.04425 / 2.96 ( 518) hydrogen bonds : angle 4.19597 / 2.97 ( 1385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 83 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7659 (mm-30) REVERT: A 163 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: A 462 GLU cc_start: 0.7703 (tp30) cc_final: 0.7146 (tp30) REVERT: A 573 GLN cc_start: 0.6751 (pp30) cc_final: 0.6265 (pp30) REVERT: A 633 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7276 (mp0) REVERT: A 660 ASP cc_start: 0.8208 (t0) cc_final: 0.7879 (t0) REVERT: A 691 GLU cc_start: 0.7525 (pm20) cc_final: 0.7238 (pm20) REVERT: A 755 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 769 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8154 (mtp85) REVERT: A 1088 VAL cc_start: 0.8242 (t) cc_final: 0.7879 (m) REVERT: A 1152 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7569 (mtmm) outliers start: 35 outliers final: 28 residues processed: 256 average time/residue: 0.1215 time to fit residues: 42.9454 Evaluate side-chains 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115044 restraints weight = 18491.884| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.88 r_work: 0.3210 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12937 Z= 0.200 Angle : 0.552 7.928 18092 Z= 0.313 Chirality : 0.040 0.215 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.834 179.447 3288 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.17 % Allowed : 24.33 % Favored : 72.50 % 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: 0.15 (0.25), residues: 1154 helix: 1.28 (0.23), residues: 542 sheet: -0.30 (0.75), residues: 50 loop : -1.06 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 103 TYR 0.025 0.002 TYR A 351 PHE 0.013 0.001 PHE A 477 TRP 0.014 0.001 TRP A 46 HIS 0.010 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (12937) covalent geometry : angle 0.55163 / 0.31 (18092) hydrogen bonds : bond 0.04472 / 2.98 ( 518) hydrogen bonds : angle 4.23551 / 3.00 ( 1385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7800 (mp) REVERT: A 39 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7708 (ptm-80) REVERT: A 83 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7664 (mm-30) REVERT: A 163 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: A 382 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.8195 (mtt-85) REVERT: A 462 GLU cc_start: 0.7703 (tp30) cc_final: 0.7143 (tp30) REVERT: A 573 GLN cc_start: 0.6781 (pp30) cc_final: 0.6283 (pp30) REVERT: A 633 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7172 (mp0) REVERT: A 660 ASP cc_start: 0.8176 (t0) cc_final: 0.7851 (t0) REVERT: A 691 GLU cc_start: 0.7486 (pm20) cc_final: 0.7231 (pm20) REVERT: A 720 ARG cc_start: 0.8338 (ttp-170) cc_final: 0.7985 (ttm110) REVERT: A 727 MET cc_start: 0.7794 (mmm) cc_final: 0.7538 (mmm) REVERT: A 755 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7536 (mm-30) REVERT: A 769 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8148 (mtp85) REVERT: A 1008 TYR cc_start: 0.8496 (m-10) cc_final: 0.8066 (m-10) REVERT: A 1152 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7552 (mtmm) outliers start: 33 outliers final: 31 residues processed: 255 average time/residue: 0.1402 time to fit residues: 49.0580 Evaluate side-chains 265 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 74 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116404 restraints weight = 18463.012| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.88 r_work: 0.3201 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12937 Z= 0.145 Angle : 0.530 10.172 18092 Z= 0.300 Chirality : 0.038 0.207 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.830 178.800 3288 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.98 % Allowed : 24.42 % Favored : 72.60 % 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: 0.19 (0.25), residues: 1154 helix: 1.33 (0.23), residues: 542 sheet: -0.37 (0.76), residues: 50 loop : -1.05 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 103 TYR 0.027 0.001 TYR A 351 PHE 0.011 0.001 PHE A 477 TRP 0.010 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12937) covalent geometry : angle 0.53042 / 0.30 (18092) hydrogen bonds : bond 0.04212 / 2.82 ( 518) hydrogen bonds : angle 4.18225 / 2.96 ( 1385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 25 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7660 (p) REVERT: A 39 ARG cc_start: 0.7988 (ptm-80) cc_final: 0.7643 (ptm-80) REVERT: A 163 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: A 462 GLU cc_start: 0.7687 (tp30) cc_final: 0.7112 (tp30) REVERT: A 573 GLN cc_start: 0.6755 (pp30) cc_final: 0.6225 (pp30) REVERT: A 633 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 660 ASP cc_start: 0.8155 (t0) cc_final: 0.7821 (t0) REVERT: A 691 GLU cc_start: 0.7465 (pm20) cc_final: 0.7211 (pm20) REVERT: A 720 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.7980 (ttm110) REVERT: A 727 MET cc_start: 0.7769 (mmm) cc_final: 0.7509 (mmm) REVERT: A 755 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 769 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8108 (mtp85) outliers start: 31 outliers final: 23 residues processed: 251 average time/residue: 0.1331 time to fit residues: 46.0237 Evaluate side-chains 255 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS ** A1235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116374 restraints weight = 18434.301| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.89 r_work: 0.3191 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12937 Z= 0.154 Angle : 0.538 9.865 18092 Z= 0.303 Chirality : 0.038 0.207 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.776 178.684 3288 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.98 % Allowed : 24.90 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.25), residues: 1154 helix: 1.34 (0.23), residues: 543 sheet: -0.49 (0.76), residues: 50 loop : -1.03 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.019 0.001 TYR A1209 PHE 0.012 0.001 PHE A 477 TRP 0.012 0.001 TRP A 46 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12937) covalent geometry : angle 0.53799 / 0.30 (18092) hydrogen bonds : bond 0.04189 / 2.81 ( 518) hydrogen bonds : angle 4.15418 / 2.94 ( 1385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.83 seconds wall clock time: 55 minutes 22.00 seconds (3322.00 seconds total)