Starting phenix.real_space_refine on Wed Feb 4 19:39:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jwk_61853/02_2026/9jwk_61853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jwk_61853/02_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_61853/02_2026/9jwk_61853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jwk_61853/02_2026/9jwk_61853.map" model { file = "/net/cci-nas-00/data/ceres_data/9jwk_61853/02_2026/9jwk_61853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jwk_61853/02_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-2.0-5952/lib/python3.9/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: 2.75, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 509.9 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: 1.55 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: 2.61 Time building geometry restraints manager: 1.38 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=" 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=" C GLU A 755 " pdb=" N PRO A 756 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.66e+00 bond pdb=" C LEU A 138 " pdb=" O LEU A 138 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.22e-02 6.72e+03 2.63e+00 ... (remaining 12932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 18005 3.34 - 6.69: 81 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=" N LEU A 304 " pdb=" CA LEU A 304 " pdb=" C LEU A 304 " ideal model delta sigma weight residual 114.56 109.51 5.05 1.27e+00 6.20e-01 1.58e+01 angle pdb=" CB MET A 727 " pdb=" CG MET A 727 " pdb=" SD MET A 727 " ideal model delta sigma weight residual 112.70 124.52 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C TYR A 136 " pdb=" CA TYR A 136 " pdb=" CB TYR A 136 " ideal model delta sigma weight residual 111.41 105.80 5.61 1.65e+00 3.67e-01 1.16e+01 angle pdb=" CA TYR A 136 " pdb=" C TYR A 136 " pdb=" O TYR A 136 " ideal model delta sigma weight residual 121.66 117.69 3.97 1.17e+00 7.31e-01 1.15e+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: 1839 0.057 - 0.114: 226 0.114 - 0.172: 21 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.330 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.003 0.050 12937 Z= 0.159 Angle : 0.614 16.716 18092 Z= 0.323 Chirality : 0.038 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 covalent geometry : bond 0.00329 (12937) covalent geometry : angle 0.61402 (18092) hydrogen bonds : bond 0.12433 ( 518) hydrogen bonds : angle 5.68289 ( 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 : 0.430 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: 0.1335 time to fit residues: 43.8466 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 : 0.399 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN 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 = 0.144056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116695 restraints weight = 18500.311| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.92 r_work: 0.3225 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12937 Z= 0.147 Angle : 0.559 6.713 18092 Z= 0.293 Chirality : 0.037 0.208 2091 Planarity : 0.004 0.041 1804 Dihedral : 19.782 178.208 3290 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.79 % Allowed : 21.15 % Favored : 76.06 % 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: 0.23 (0.25), residues: 1154 helix: 1.20 (0.23), residues: 538 sheet: 0.13 (0.78), residues: 54 loop : -0.88 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.017 0.001 TYR A1209 PHE 0.007 0.001 PHE A 631 TRP 0.014 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00316 (12937) covalent geometry : angle 0.55859 (18092) hydrogen bonds : bond 0.04126 ( 518) hydrogen bonds : angle 4.38582 ( 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 281 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 163 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: A 389 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8169 (mmtm) REVERT: A 462 GLU cc_start: 0.7789 (tp30) cc_final: 0.7215 (tp30) REVERT: A 660 ASP cc_start: 0.8167 (t0) cc_final: 0.7830 (t0) REVERT: A 755 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 769 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8167 (mtp85) REVERT: A 781 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7937 (tp30) REVERT: A 1152 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7572 (mtmm) outliers start: 29 outliers final: 13 residues processed: 265 average time/residue: 0.1376 time to fit residues: 49.8914 Evaluate side-chains 256 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 163 GLN 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 489 THR 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 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1186 VAL 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: 0.6980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3730 r_free = 0.3730 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115446 restraints weight = 18627.270| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.91 r_work: 0.3216 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12937 Z= 0.179 Angle : 0.568 8.859 18092 Z= 0.297 Chirality : 0.038 0.222 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.731 179.400 3288 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.98 % Allowed : 22.79 % Favored : 74.23 % 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: 1.20 (0.23), residues: 542 sheet: 0.23 (0.82), residues: 44 loop : -0.95 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.017 0.001 TYR A 377 PHE 0.007 0.001 PHE A 993 TRP 0.015 0.001 TRP A 46 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00389 (12937) covalent geometry : angle 0.56843 (18092) hydrogen bonds : bond 0.04124 ( 518) hydrogen bonds : angle 4.29304 ( 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 278 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 83 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7631 (mm-30) REVERT: A 462 GLU cc_start: 0.7738 (tp30) cc_final: 0.7176 (tp30) REVERT: A 660 ASP cc_start: 0.8206 (t0) cc_final: 0.7877 (t0) REVERT: A 691 GLU cc_start: 0.7509 (pm20) cc_final: 0.7214 (pm20) REVERT: A 755 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 769 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8166 (mtp85) REVERT: A 1008 TYR cc_start: 0.8554 (m-10) cc_final: 0.8038 (m-10) REVERT: A 1152 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7570 (mtmm) REVERT: A 1256 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7621 (mtmm) outliers start: 31 outliers final: 19 residues processed: 266 average time/residue: 0.1369 time to fit residues: 49.1533 Evaluate side-chains 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 115 TYR 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 498 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 1013 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.141332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113821 restraints weight = 18673.274| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.90 r_work: 0.3170 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12937 Z= 0.213 Angle : 0.591 7.069 18092 Z= 0.307 Chirality : 0.039 0.220 2091 Planarity : 0.004 0.044 1804 Dihedral : 19.734 179.407 3288 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.75 % Allowed : 22.69 % Favored : 73.56 % 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: 1.21 (0.23), residues: 542 sheet: 0.17 (0.82), residues: 43 loop : -1.00 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.026 0.002 TYR A 351 PHE 0.008 0.001 PHE A 631 TRP 0.016 0.001 TRP A 46 HIS 0.010 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00466 (12937) covalent geometry : angle 0.59088 (18092) hydrogen bonds : bond 0.04241 ( 518) hydrogen bonds : angle 4.29083 ( 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 289 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 60 ARG cc_start: 0.7950 (ttt180) cc_final: 0.7713 (ttt180) REVERT: A 163 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 462 GLU cc_start: 0.7720 (tp30) cc_final: 0.7147 (tp30) REVERT: A 660 ASP cc_start: 0.8219 (t0) cc_final: 0.7891 (t0) REVERT: A 691 GLU cc_start: 0.7556 (pm20) cc_final: 0.7268 (pm20) REVERT: A 727 MET cc_start: 0.7842 (mmm) cc_final: 0.7517 (mmm) REVERT: A 755 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 1008 TYR cc_start: 0.8504 (m-10) cc_final: 0.8032 (m-10) REVERT: A 1152 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7573 (mtmm) REVERT: A 1208 TYR cc_start: 0.8302 (m-10) cc_final: 0.8008 (m-10) REVERT: A 1256 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7629 (mtmm) outliers start: 39 outliers final: 26 residues processed: 270 average time/residue: 0.1357 time to fit residues: 49.7396 Evaluate side-chains 274 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 115 TYR 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 411 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 645 LYS Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 713 VAL 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 793 ILE Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1200 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 111 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 chunk 99 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3754 r_free = 0.3754 target = 0.144273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116851 restraints weight = 18777.662| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.94 r_work: 0.3231 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12937 Z= 0.125 Angle : 0.538 11.414 18092 Z= 0.279 Chirality : 0.036 0.214 2091 Planarity : 0.004 0.044 1804 Dihedral : 19.650 178.367 3288 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.56 % Allowed : 23.27 % Favored : 73.17 % 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: 0.34 (0.25), residues: 1154 helix: 1.42 (0.23), residues: 541 sheet: 0.19 (0.82), residues: 43 loop : -0.96 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.011 0.001 TYR A1015 PHE 0.013 0.001 PHE A 477 TRP 0.009 0.001 TRP A 46 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00269 (12937) covalent geometry : angle 0.53761 (18092) hydrogen bonds : bond 0.03678 ( 518) hydrogen bonds : angle 4.06025 ( 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 276 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 25 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 115 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5878 (p90) REVERT: A 163 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: A 462 GLU cc_start: 0.7756 (tp30) cc_final: 0.7178 (tp30) REVERT: A 573 GLN cc_start: 0.6711 (pp30) cc_final: 0.6281 (pp30) REVERT: A 660 ASP cc_start: 0.8183 (t0) cc_final: 0.7838 (t0) REVERT: A 691 GLU cc_start: 0.7458 (pm20) cc_final: 0.7169 (pm20) REVERT: A 755 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 1008 TYR cc_start: 0.8539 (m-10) cc_final: 0.8069 (m-10) REVERT: A 1082 PHE cc_start: 0.8572 (m-80) cc_final: 0.8312 (m-80) REVERT: A 1256 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7634 (mtmm) outliers start: 37 outliers final: 22 residues processed: 260 average time/residue: 0.1074 time to fit residues: 38.6245 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 : 0.324 ------------------------------------------------------------------------------- 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 496 TRP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 667 ARG 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 1013 ASP Chi-restraints excluded: chain A residue 1111 LYS 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 Chi-restraints excluded: chain A residue 1339 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3725 r_free = 0.3725 target = 0.142142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114661 restraints weight = 18593.544| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.90 r_work: 0.3204 rms_B_bonded: 2.70 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: 0.7700 moved from start: 0.1477 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= 0.192 Angle : 0.574 7.817 18092 Z= 0.298 Chirality : 0.038 0.212 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.645 179.815 3288 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.37 % Allowed : 23.46 % Favored : 73.17 % 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: 0.23 (0.25), residues: 1154 helix: 1.33 (0.23), residues: 543 sheet: 0.07 (0.81), residues: 43 loop : -1.02 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 60 TYR 0.031 0.002 TYR A 351 PHE 0.011 0.001 PHE A 477 TRP 0.013 0.001 TRP A 46 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00420 (12937) covalent geometry : angle 0.57414 (18092) hydrogen bonds : bond 0.04052 ( 518) hydrogen bonds : angle 4.14274 ( 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 271 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 25 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7908 (p) REVERT: A 163 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: A 356 TYR cc_start: 0.8241 (t80) cc_final: 0.7977 (t80) REVERT: A 573 GLN cc_start: 0.6754 (pp30) cc_final: 0.6291 (pp30) REVERT: A 633 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7173 (mp0) REVERT: A 660 ASP cc_start: 0.8201 (t0) cc_final: 0.7853 (t0) REVERT: A 691 GLU cc_start: 0.7542 (pm20) cc_final: 0.7278 (pm20) REVERT: A 701 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 755 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 769 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8160 (mtp85) REVERT: A 1008 TYR cc_start: 0.8542 (m-10) cc_final: 0.8040 (m-10) REVERT: A 1082 PHE cc_start: 0.8620 (m-80) cc_final: 0.8387 (m-80) REVERT: A 1152 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7594 (mtmm) REVERT: A 1256 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7629 (mtmm) outliers start: 35 outliers final: 28 residues processed: 259 average time/residue: 0.1293 time to fit residues: 45.4227 Evaluate side-chains 267 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 496 TRP 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 598 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 667 ARG 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 779 LEU 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 1278 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1323 SER 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: 0.8980 chunk 25 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN 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 = 0.3743 r_free = 0.3743 target = 0.143464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115808 restraints weight = 18619.653| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.92 r_work: 0.3227 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12937 Z= 0.142 Angle : 0.554 10.026 18092 Z= 0.287 Chirality : 0.036 0.214 2091 Planarity : 0.004 0.057 1804 Dihedral : 19.547 178.912 3288 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.75 % Allowed : 23.56 % 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: 0.29 (0.25), residues: 1154 helix: 1.41 (0.23), residues: 543 sheet: -0.14 (0.75), residues: 50 loop : -1.02 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 60 TYR 0.025 0.001 TYR A 351 PHE 0.008 0.001 PHE A 631 TRP 0.009 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00310 (12937) covalent geometry : angle 0.55432 (18092) hydrogen bonds : bond 0.03746 ( 518) hydrogen bonds : angle 4.05669 ( 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 270 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 25 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 163 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: A 356 TYR cc_start: 0.8188 (t80) cc_final: 0.7896 (t80) REVERT: A 389 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8113 (mmtm) REVERT: A 462 GLU cc_start: 0.7709 (tp30) cc_final: 0.7156 (tp30) REVERT: A 573 GLN cc_start: 0.6767 (pp30) cc_final: 0.6278 (pp30) REVERT: A 633 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7198 (mp0) REVERT: A 660 ASP cc_start: 0.8154 (t0) cc_final: 0.7804 (t0) REVERT: A 691 GLU cc_start: 0.7456 (pm20) cc_final: 0.7192 (pm20) REVERT: A 701 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 717 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8122 (ttt-90) REVERT: A 720 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7964 (ttm170) REVERT: A 727 MET cc_start: 0.7793 (mmm) cc_final: 0.7520 (mmm) REVERT: A 755 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 769 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8132 (mtp85) REVERT: A 1082 PHE cc_start: 0.8590 (m-80) cc_final: 0.8363 (m-80) REVERT: A 1152 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7557 (mtmm) REVERT: A 1256 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7629 (mtmm) outliers start: 39 outliers final: 27 residues processed: 255 average time/residue: 0.1284 time to fit residues: 44.8319 Evaluate side-chains 259 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 496 TRP 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 598 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 9 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 163 GLN A 414 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1177 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116304 restraints weight = 18663.203| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.92 r_work: 0.3218 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12937 Z= 0.143 Angle : 0.549 9.729 18092 Z= 0.285 Chirality : 0.036 0.214 2091 Planarity : 0.005 0.112 1804 Dihedral : 19.498 178.441 3288 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.46 % Allowed : 23.94 % 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: 0.33 (0.25), residues: 1154 helix: 1.44 (0.23), residues: 542 sheet: 0.01 (0.81), residues: 43 loop : -0.99 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 60 TYR 0.034 0.001 TYR A 351 PHE 0.008 0.001 PHE A 456 TRP 0.010 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00313 (12937) covalent geometry : angle 0.54939 (18092) hydrogen bonds : bond 0.03738 ( 518) hydrogen bonds : angle 4.04241 ( 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 269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 25 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7933 (p) REVERT: A 163 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: A 356 TYR cc_start: 0.8144 (t80) cc_final: 0.7837 (t80) REVERT: A 389 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8074 (mmtm) REVERT: A 462 GLU cc_start: 0.7730 (tp30) cc_final: 0.7169 (tp30) REVERT: A 573 GLN cc_start: 0.6740 (pp30) cc_final: 0.6250 (pp30) REVERT: A 633 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7069 (mp0) REVERT: A 660 ASP cc_start: 0.8166 (t0) cc_final: 0.7819 (t0) REVERT: A 691 GLU cc_start: 0.7490 (pm20) cc_final: 0.7232 (pm20) REVERT: A 717 ARG cc_start: 0.8503 (mtp180) cc_final: 0.8269 (ttt-90) REVERT: A 720 ARG cc_start: 0.8338 (ttm110) cc_final: 0.8055 (ttm110) REVERT: A 727 MET cc_start: 0.7838 (mmm) cc_final: 0.7531 (mmm) REVERT: A 755 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 769 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8150 (mtp85) REVERT: A 1082 PHE cc_start: 0.8598 (m-80) cc_final: 0.8374 (m-80) REVERT: A 1152 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7558 (mtmm) REVERT: A 1256 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7632 (mtmm) outliers start: 36 outliers final: 29 residues processed: 253 average time/residue: 0.1370 time to fit residues: 47.1373 Evaluate side-chains 258 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 186 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 496 TRP 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 598 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1323 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117322 restraints weight = 18611.351| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.91 r_work: 0.3246 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12937 Z= 0.125 Angle : 0.544 8.394 18092 Z= 0.284 Chirality : 0.036 0.212 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.453 177.762 3288 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.46 % Allowed : 24.33 % Favored : 72.21 % 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: 0.35 (0.25), residues: 1154 helix: 1.47 (0.23), residues: 543 sheet: -0.24 (0.75), residues: 50 loop : -0.98 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 103 TYR 0.036 0.001 TYR A 351 PHE 0.020 0.001 PHE A 477 TRP 0.008 0.001 TRP A 46 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00273 (12937) covalent geometry : angle 0.54386 (18092) hydrogen bonds : bond 0.03594 ( 518) hydrogen bonds : angle 4.01679 ( 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 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 25 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 163 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: A 230 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5866 (mm) REVERT: A 356 TYR cc_start: 0.8098 (t80) cc_final: 0.7786 (t80) REVERT: A 389 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8057 (mmtm) REVERT: A 409 GLU cc_start: 0.7577 (mp0) cc_final: 0.7332 (mp0) REVERT: A 530 LEU cc_start: 0.8380 (mt) cc_final: 0.8179 (mm) REVERT: A 573 GLN cc_start: 0.6738 (pp30) cc_final: 0.6237 (pp30) REVERT: A 633 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6982 (mp0) REVERT: A 660 ASP cc_start: 0.8141 (t0) cc_final: 0.7798 (t0) REVERT: A 691 GLU cc_start: 0.7433 (pm20) cc_final: 0.7177 (pm20) REVERT: A 701 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7648 (pt0) REVERT: A 717 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8214 (ttt-90) REVERT: A 720 ARG cc_start: 0.8315 (ttm110) cc_final: 0.8055 (ttm110) REVERT: A 755 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 769 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8133 (mtp85) REVERT: A 771 MET cc_start: 0.7470 (ttp) cc_final: 0.7264 (ttp) REVERT: A 997 PHE cc_start: 0.7240 (m-80) cc_final: 0.7035 (m-80) REVERT: A 1082 PHE cc_start: 0.8577 (m-80) cc_final: 0.8347 (m-80) REVERT: A 1088 VAL cc_start: 0.8244 (t) cc_final: 0.7858 (m) REVERT: A 1152 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7541 (mtmm) REVERT: A 1225 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 1256 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7616 (mtmm) outliers start: 36 outliers final: 30 residues processed: 244 average time/residue: 0.1316 time to fit residues: 44.1230 Evaluate side-chains 256 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 186 GLN Chi-restraints excluded: chain A residue 230 LEU 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 496 TRP 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 598 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1340 ILE 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: 2.9990 chunk 112 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 HIS A1160 ASN A1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113893 restraints weight = 18636.770| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.90 r_work: 0.3194 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12937 Z= 0.226 Angle : 0.612 8.144 18092 Z= 0.317 Chirality : 0.040 0.214 2091 Planarity : 0.004 0.042 1804 Dihedral : 19.493 179.898 3288 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.37 % Allowed : 24.62 % Favored : 72.02 % 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: 0.22 (0.25), residues: 1154 helix: 1.35 (0.23), residues: 543 sheet: -0.35 (0.74), residues: 50 loop : -1.03 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 103 TYR 0.036 0.002 TYR A 351 PHE 0.013 0.001 PHE A 456 TRP 0.015 0.002 TRP A 46 HIS 0.009 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00495 (12937) covalent geometry : angle 0.61164 (18092) hydrogen bonds : bond 0.04238 ( 518) hydrogen bonds : angle 4.15044 ( 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 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 25 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 230 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5931 (mm) REVERT: A 356 TYR cc_start: 0.8181 (t80) cc_final: 0.7901 (t80) REVERT: A 409 GLU cc_start: 0.7615 (mp0) cc_final: 0.7385 (mp0) REVERT: A 573 GLN cc_start: 0.6741 (pp30) cc_final: 0.6237 (pp30) REVERT: A 585 PHE cc_start: 0.7732 (m-80) cc_final: 0.7432 (m-80) REVERT: A 633 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7118 (mp0) REVERT: A 660 ASP cc_start: 0.8214 (t0) cc_final: 0.7875 (t0) REVERT: A 691 GLU cc_start: 0.7501 (pm20) cc_final: 0.7249 (pm20) REVERT: A 701 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7770 (pt0) REVERT: A 717 ARG cc_start: 0.8485 (mtp180) cc_final: 0.8231 (ttt-90) REVERT: A 720 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7893 (ttm170) REVERT: A 727 MET cc_start: 0.7835 (mmm) cc_final: 0.7543 (mmm) REVERT: A 755 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 769 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8152 (mtp85) REVERT: A 771 MET cc_start: 0.7540 (ttp) cc_final: 0.7293 (ttp) REVERT: A 1152 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7503 (mtmm) REVERT: A 1225 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 1256 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7641 (mtmm) outliers start: 35 outliers final: 31 residues processed: 247 average time/residue: 0.1273 time to fit residues: 42.5487 Evaluate side-chains 257 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 186 GLN Chi-restraints excluded: chain A residue 230 LEU 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 496 TRP 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 598 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ASN Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1340 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 HIS A1160 ASN A1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116228 restraints weight = 18594.592| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.91 r_work: 0.3234 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12937 Z= 0.145 Angle : 0.573 11.572 18092 Z= 0.297 Chirality : 0.037 0.207 2091 Planarity : 0.004 0.043 1804 Dihedral : 19.451 179.212 3288 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.46 % Allowed : 24.52 % Favored : 72.02 % 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: 0.33 (0.25), residues: 1154 helix: 1.48 (0.23), residues: 537 sheet: -0.34 (0.74), residues: 50 loop : -0.99 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 103 TYR 0.037 0.001 TYR A 351 PHE 0.014 0.001 PHE A 456 TRP 0.010 0.001 TRP A 46 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00321 (12937) covalent geometry : angle 0.57335 (18092) hydrogen bonds : bond 0.03791 ( 518) hydrogen bonds : angle 4.04196 ( 1385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.47 seconds wall clock time: 53 minutes 32.19 seconds (3212.19 seconds total)