Starting phenix.real_space_refine on Wed Sep 17 23:03:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.map" model { file = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtc_0061/09_2025/6gtc_0061.cif" } resolution = 3.91 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 22 5.16 5 C 7423 2.51 5 N 1994 2.21 5 O 2427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11931 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10575 Classifications: {'peptide': 1280} Link IDs: {'PTRANS': 27, 'TRANS': 1252} Chain breaks: 3 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 8, 'rna3p': 19} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 2.50, per 1000 atoms: 0.21 Number of scatterers: 11931 At special positions: 0 Unit cell: (94.016, 124.8, 110.656, 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 22 16.00 P 65 15.00 O 2427 8.00 N 1994 7.00 C 7423 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: 1.03 Conformation dependent library (CDL) restraints added in 414.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 38.0% alpha, 7.7% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.562A pdb=" N GLN A 5 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 6 " --> pdb=" O ILE A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 6' Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.850A pdb=" N ASN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.700A pdb=" N GLU A 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.799A pdb=" N ASP A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.747A pdb=" N TYR A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.724A pdb=" N THR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.806A pdb=" N LYS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.749A pdb=" N LEU A 127 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 4.018A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.555A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.580A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.663A pdb=" N ALA A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 removed outlier: 3.690A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.615A pdb=" N ILE A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.689A pdb=" N TYR A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLN A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.776A pdb=" N LEU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.635A pdb=" N LEU A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.817A pdb=" N LEU A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.532A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.607A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.964A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 removed outlier: 3.851A pdb=" N VAL A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.851A pdb=" N ASN A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.632A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.773A pdb=" N TYR A 682 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 683 " --> pdb=" O LYS A 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 683' Processing helix chain 'A' and resid 685 through 695 removed outlier: 4.812A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.964A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.792A pdb=" N TYR A 747 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 758 removed outlier: 3.663A pdb=" N ARG A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.917A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 811 Processing helix chain 'A' and resid 813 through 819 removed outlier: 4.266A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.574A pdb=" N ASN A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 removed outlier: 4.129A pdb=" N GLU A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 908 " --> pdb=" O LYS A 905 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN A 909 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 911 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 959 Processing helix chain 'A' and resid 970 through 994 removed outlier: 3.790A pdb=" N ILE A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 978 " --> pdb=" O ILE A 974 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1021 through 1026 removed outlier: 3.785A pdb=" N GLN A1025 " --> pdb=" O LYS A1021 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A1026 " --> pdb=" O GLN A1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1021 through 1026' Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.713A pdb=" N GLY A1068 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1112 removed outlier: 3.914A pdb=" N GLU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.688A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1133 " --> pdb=" O TYR A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1129 through 1133' Processing helix chain 'A' and resid 1169 through 1180 Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.530A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.853A pdb=" N PHE A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1208 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.790A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1275 removed outlier: 3.779A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1270 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 3.691A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.567A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 788 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.567A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.912A pdb=" N PHE A 244 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG A 256 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 removed outlier: 4.037A pdb=" N LYS A 288 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 297 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR A 295 " --> pdb=" O VAL A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 661 removed outlier: 3.621A pdb=" N THR A 765 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 841 through 843 Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 929 removed outlier: 7.211A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 943 through 944 Processing sheet with id=AB1, first strand: chain 'A' and resid 1003 through 1006 removed outlier: 6.788A pdb=" N VAL A1003 " --> pdb=" O TYR A1075 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A1077 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A1005 " --> pdb=" O VAL A1077 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 3.700A pdb=" N LYS A1114 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1150 through 1153 removed outlier: 3.758A pdb=" N ARG A1150 " --> pdb=" O VAL A1168 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A1168 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A1152 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A1166 " --> pdb=" O ILE A1152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1219 through 1220 removed outlier: 4.334A pdb=" N ASN A1219 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A1228 " --> pdb=" O ASN A1219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 231 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3054 1.33 - 1.45: 2553 1.45 - 1.57: 6533 1.57 - 1.69: 127 1.69 - 1.81: 35 Bond restraints: 12302 Sorted by residual: bond pdb=" C VAL A 576 " pdb=" N PRO A 577 " ideal model delta sigma weight residual 1.331 1.400 -0.068 7.90e-03 1.60e+04 7.51e+01 bond pdb=" C VAL A1168 " pdb=" N TYR A1169 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.07e-02 2.33e+03 1.22e+01 bond pdb=" CA LYS A1034 " pdb=" CB LYS A1034 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.39e-02 5.18e+03 4.84e+00 bond pdb=" C3' DG C -7 " pdb=" O3' DG C -7 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CA ASP A 947 " pdb=" C ASP A 947 " ideal model delta sigma weight residual 1.522 1.555 -0.034 1.72e-02 3.38e+03 3.84e+00 ... (remaining 12297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 16589 3.20 - 6.39: 190 6.39 - 9.59: 36 9.59 - 12.78: 6 12.78 - 15.98: 1 Bond angle restraints: 16822 Sorted by residual: angle pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" C ILE A 105 " ideal model delta sigma weight residual 113.53 107.60 5.93 9.80e-01 1.04e+00 3.66e+01 angle pdb=" N VAL A 523 " pdb=" CA VAL A 523 " pdb=" C VAL A 523 " ideal model delta sigma weight residual 112.96 107.00 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" N ILE A 65 " pdb=" CA ILE A 65 " pdb=" C ILE A 65 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" C LYS A 869 " pdb=" N ASP A 870 " pdb=" CA ASP A 870 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" N ILE A 913 " pdb=" CA ILE A 913 " pdb=" C ILE A 913 " ideal model delta sigma weight residual 108.93 115.48 -6.55 1.35e+00 5.49e-01 2.36e+01 ... (remaining 16817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 6837 25.06 - 50.11: 435 50.11 - 75.17: 107 75.17 - 100.23: 13 100.23 - 125.28: 1 Dihedral angle restraints: 7393 sinusoidal: 3596 harmonic: 3797 Sorted by residual: dihedral pdb=" CA GLU A 614 " pdb=" C GLU A 614 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 7390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1737 0.105 - 0.210: 84 0.210 - 0.315: 5 0.315 - 0.420: 1 0.420 - 0.525: 1 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CB ILE A1002 " pdb=" CA ILE A1002 " pdb=" CG1 ILE A1002 " pdb=" CG2 ILE A1002 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CB ILE A1074 " pdb=" CA ILE A1074 " pdb=" CG1 ILE A1074 " pdb=" CG2 ILE A1074 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB VAL A 576 " pdb=" CA VAL A 576 " pdb=" CG1 VAL A 576 " pdb=" CG2 VAL A 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1825 not shown) Planarity restraints: 1925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 614 " 0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 615 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 615 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 615 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 670 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 272 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C TYR A 272 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 272 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 273 " 0.019 2.00e-02 2.50e+03 ... (remaining 1922 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3158 2.80 - 3.32: 10135 3.32 - 3.85: 19859 3.85 - 4.37: 23088 4.37 - 4.90: 37513 Nonbonded interactions: 93753 Sorted by model distance: nonbonded pdb=" OD1 ASN A 825 " pdb=" OG1 THR A 885 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 83 " pdb=" O PRO A 209 " model vdw 2.278 3.040 nonbonded pdb=" O PHE A 941 " pdb=" OH TYR A 984 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 392 " pdb=" OD1 ASP A 556 " model vdw 2.301 3.040 nonbonded pdb=" O LEU A 418 " pdb=" OG1 THR A 422 " model vdw 2.316 3.040 ... (remaining 93748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12302 Z= 0.217 Angle : 0.945 15.978 16822 Z= 0.504 Chirality : 0.054 0.525 1828 Planarity : 0.006 0.090 1925 Dihedral : 16.563 125.283 4939 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.86 % Allowed : 7.73 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 aren not related in a simple way. whole: -5.69 (0.16), residues: 1272 helix: -4.79 (0.08), residues: 474 sheet: -2.79 (0.51), residues: 95 loop : -3.23 (0.18), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 833 TYR 0.021 0.002 TYR A 272 PHE 0.027 0.002 PHE A 258 TRP 0.036 0.003 TRP A 971 HIS 0.008 0.002 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00425 (12302) covalent geometry : angle 0.94475 (16822) hydrogen bonds : bond 0.34175 ( 235) hydrogen bonds : angle 11.30654 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 ILE cc_start: 0.7326 (mp) cc_final: 0.6581 (mm) REVERT: A 920 GLU cc_start: 0.4849 (mt-10) cc_final: 0.4203 (mt-10) REVERT: A 1027 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (tt) outliers start: 10 outliers final: 0 residues processed: 268 average time/residue: 0.1270 time to fit residues: 47.0113 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN A 78 ASN A 126 ASN A 305 ASN A 395 ASN A 538 HIS A 588 GLN A 790 ASN A 843 HIS A 851 ASN A 853 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144152 restraints weight = 16680.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143599 restraints weight = 21284.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147182 restraints weight = 18359.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146690 restraints weight = 12760.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146952 restraints weight = 12548.283| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12302 Z= 0.175 Angle : 0.701 12.292 16822 Z= 0.376 Chirality : 0.045 0.239 1828 Planarity : 0.005 0.076 1925 Dihedral : 19.087 127.253 2201 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.35 % Allowed : 11.34 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 aren not related in a simple way. whole: -4.86 (0.18), residues: 1272 helix: -3.69 (0.15), residues: 508 sheet: -2.65 (0.48), residues: 109 loop : -2.92 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 918 TYR 0.018 0.002 TYR A 11 PHE 0.018 0.002 PHE A1061 TRP 0.017 0.002 TRP A 971 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00382 (12302) covalent geometry : angle 0.70083 (16822) hydrogen bonds : bond 0.06247 ( 235) hydrogen bonds : angle 6.46903 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7883 (t0) REVERT: A 311 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6442 (mp) REVERT: A 352 MET cc_start: 0.6888 (ttm) cc_final: 0.6617 (ttm) REVERT: A 688 ILE cc_start: 0.7491 (mp) cc_final: 0.7252 (mt) REVERT: A 888 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 949 MET cc_start: 0.6381 (mmm) cc_final: 0.6058 (mmm) REVERT: A 1217 MET cc_start: 0.5623 (mmp) cc_final: 0.5420 (mmt) REVERT: A 1221 LYS cc_start: 0.5862 (tptp) cc_final: 0.5598 (tptp) outliers start: 39 outliers final: 20 residues processed: 188 average time/residue: 0.1118 time to fit residues: 30.0785 Evaluate side-chains 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 HIS ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A 851 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145548 restraints weight = 16647.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145641 restraints weight = 18660.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148845 restraints weight = 16761.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148725 restraints weight = 11857.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149134 restraints weight = 11422.713| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12302 Z= 0.126 Angle : 0.650 18.640 16822 Z= 0.339 Chirality : 0.042 0.202 1828 Planarity : 0.004 0.071 1925 Dihedral : 19.129 133.343 2199 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.75 % Allowed : 14.18 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 aren not related in a simple way. whole: -4.22 (0.20), residues: 1272 helix: -3.09 (0.17), residues: 515 sheet: -2.27 (0.52), residues: 95 loop : -2.62 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 872 TYR 0.021 0.001 TYR A 47 PHE 0.024 0.001 PHE A 182 TRP 0.013 0.002 TRP A 971 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00274 (12302) covalent geometry : angle 0.65028 (16822) hydrogen bonds : bond 0.05289 ( 235) hydrogen bonds : angle 5.68846 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8070 (t0) cc_final: 0.7851 (t0) REVERT: A 311 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6579 (mp) REVERT: A 345 ASP cc_start: 0.7060 (m-30) cc_final: 0.6857 (m-30) REVERT: A 581 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8696 (ttmm) REVERT: A 688 ILE cc_start: 0.7487 (mp) cc_final: 0.7285 (mt) REVERT: A 689 LEU cc_start: 0.8018 (mm) cc_final: 0.7614 (tp) REVERT: A 785 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6925 (tt) outliers start: 32 outliers final: 15 residues processed: 177 average time/residue: 0.1142 time to fit residues: 28.5780 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 0.0980 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS A 851 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149227 restraints weight = 16402.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149336 restraints weight = 21926.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150939 restraints weight = 17398.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151076 restraints weight = 13916.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152271 restraints weight = 12866.662| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12302 Z= 0.111 Angle : 0.608 14.092 16822 Z= 0.317 Chirality : 0.041 0.203 1828 Planarity : 0.004 0.067 1925 Dihedral : 19.073 134.065 2199 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.92 % Allowed : 15.98 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 aren not related in a simple way. whole: -3.68 (0.21), residues: 1272 helix: -2.64 (0.19), residues: 513 sheet: -1.74 (0.55), residues: 95 loop : -2.37 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.016 0.001 TYR A 47 PHE 0.015 0.001 PHE A 182 TRP 0.012 0.001 TRP A 609 HIS 0.010 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00240 (12302) covalent geometry : angle 0.60793 (16822) hydrogen bonds : bond 0.05582 ( 235) hydrogen bonds : angle 5.12227 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7854 (t0) cc_final: 0.7650 (t0) REVERT: A 311 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6596 (mp) REVERT: A 345 ASP cc_start: 0.6740 (m-30) cc_final: 0.6012 (t0) REVERT: A 487 MET cc_start: 0.7403 (pmm) cc_final: 0.7066 (pmm) REVERT: A 570 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: A 581 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: A 689 LEU cc_start: 0.7971 (mm) cc_final: 0.7438 (mt) REVERT: A 789 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7255 (p90) REVERT: A 964 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5461 (pmt100) REVERT: A 1066 LYS cc_start: 0.7082 (mtpm) cc_final: 0.6655 (mptt) outliers start: 34 outliers final: 13 residues processed: 177 average time/residue: 0.1129 time to fit residues: 28.6854 Evaluate side-chains 148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 120 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142635 restraints weight = 16668.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141605 restraints weight = 19201.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144077 restraints weight = 17304.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143972 restraints weight = 13206.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144289 restraints weight = 12663.531| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12302 Z= 0.152 Angle : 0.637 12.468 16822 Z= 0.332 Chirality : 0.042 0.180 1828 Planarity : 0.004 0.064 1925 Dihedral : 19.106 133.712 2199 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.35 % Allowed : 16.24 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.21), residues: 1272 helix: -2.36 (0.20), residues: 513 sheet: -1.76 (0.56), residues: 95 loop : -2.25 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 202 TYR 0.017 0.001 TYR A 11 PHE 0.020 0.002 PHE A 941 TRP 0.014 0.001 TRP A1163 HIS 0.009 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00345 (12302) covalent geometry : angle 0.63706 (16822) hydrogen bonds : bond 0.04616 ( 235) hydrogen bonds : angle 5.01725 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7947 (t0) cc_final: 0.7744 (t0) REVERT: A 311 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6656 (mp) REVERT: A 345 ASP cc_start: 0.7285 (m-30) cc_final: 0.6601 (t0) REVERT: A 487 MET cc_start: 0.7580 (pmm) cc_final: 0.7329 (pmm) REVERT: A 689 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7605 (tp) REVERT: A 785 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7039 (tt) REVERT: A 789 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7410 (p90) REVERT: A 964 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5471 (ppt170) REVERT: A 1066 LYS cc_start: 0.7185 (mtpm) cc_final: 0.6800 (mptt) outliers start: 39 outliers final: 23 residues processed: 164 average time/residue: 0.1153 time to fit residues: 27.1695 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 42 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146304 restraints weight = 16520.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145975 restraints weight = 19659.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148152 restraints weight = 16799.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148050 restraints weight = 13480.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148191 restraints weight = 12446.352| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12302 Z= 0.116 Angle : 0.598 12.317 16822 Z= 0.311 Chirality : 0.041 0.185 1828 Planarity : 0.004 0.063 1925 Dihedral : 19.106 134.313 2199 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.01 % Allowed : 16.49 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.22), residues: 1272 helix: -2.04 (0.21), residues: 515 sheet: -1.53 (0.58), residues: 95 loop : -2.15 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1166 TYR 0.014 0.001 TYR A 47 PHE 0.029 0.001 PHE A 941 TRP 0.016 0.001 TRP A1163 HIS 0.014 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00258 (12302) covalent geometry : angle 0.59768 (16822) hydrogen bonds : bond 0.05152 ( 235) hydrogen bonds : angle 4.79348 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.5888 (mp0) cc_final: 0.5283 (tt0) REVERT: A 311 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6621 (mp) REVERT: A 345 ASP cc_start: 0.6918 (m-30) cc_final: 0.6292 (t0) REVERT: A 570 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: A 689 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 964 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5501 (ppt170) REVERT: A 1066 LYS cc_start: 0.7279 (mtpm) cc_final: 0.6822 (mptt) REVERT: A 1177 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7263 (tm) outliers start: 35 outliers final: 20 residues processed: 172 average time/residue: 0.1151 time to fit residues: 28.2123 Evaluate side-chains 157 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 30 optimal weight: 9.9990 chunk 119 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 66 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 694 HIS A 697 HIS A 760 GLN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149297 restraints weight = 16454.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148339 restraints weight = 20469.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149600 restraints weight = 18494.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149880 restraints weight = 14301.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150208 restraints weight = 13497.132| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12302 Z= 0.115 Angle : 0.598 11.717 16822 Z= 0.311 Chirality : 0.041 0.206 1828 Planarity : 0.004 0.061 1925 Dihedral : 19.151 134.158 2199 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.58 % Allowed : 17.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.22), residues: 1272 helix: -1.88 (0.22), residues: 519 sheet: -1.45 (0.58), residues: 95 loop : -2.09 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.014 0.001 TYR A 11 PHE 0.019 0.001 PHE A 888 TRP 0.017 0.001 TRP A1163 HIS 0.009 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00253 (12302) covalent geometry : angle 0.59781 (16822) hydrogen bonds : bond 0.05049 ( 235) hydrogen bonds : angle 4.66887 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.5767 (mp0) cc_final: 0.5342 (tt0) REVERT: A 311 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6545 (mp) REVERT: A 570 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: A 689 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7559 (mt) REVERT: A 785 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6957 (tt) REVERT: A 964 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5550 (ppt170) REVERT: A 1066 LYS cc_start: 0.7257 (mtpm) cc_final: 0.6827 (mptt) REVERT: A 1177 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7230 (tm) REVERT: A 1244 ARG cc_start: 0.6710 (mpp80) cc_final: 0.6352 (mpp80) outliers start: 30 outliers final: 19 residues processed: 157 average time/residue: 0.1085 time to fit residues: 24.7676 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.173378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141643 restraints weight = 16708.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141126 restraints weight = 19645.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143906 restraints weight = 17892.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143477 restraints weight = 12939.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143764 restraints weight = 13008.018| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12302 Z= 0.171 Angle : 0.665 13.715 16822 Z= 0.344 Chirality : 0.044 0.225 1828 Planarity : 0.004 0.077 1925 Dihedral : 19.296 134.009 2199 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.92 % Allowed : 17.96 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.22), residues: 1272 helix: -1.82 (0.22), residues: 512 sheet: -1.61 (0.55), residues: 97 loop : -2.02 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 833 TYR 0.017 0.001 TYR A 11 PHE 0.018 0.002 PHE A 888 TRP 0.017 0.002 TRP A1163 HIS 0.010 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00398 (12302) covalent geometry : angle 0.66527 (16822) hydrogen bonds : bond 0.04466 ( 235) hydrogen bonds : angle 4.80760 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7409 (p0) cc_final: 0.7128 (p0) REVERT: A 311 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6572 (mp) REVERT: A 570 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: A 689 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7534 (tp) REVERT: A 785 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7046 (tt) REVERT: A 789 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7600 (p90) REVERT: A 964 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5488 (ppt170) REVERT: A 1066 LYS cc_start: 0.7424 (mtpm) cc_final: 0.6899 (mptt) REVERT: A 1177 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7380 (tm) REVERT: A 1178 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5833 (mp) outliers start: 34 outliers final: 22 residues processed: 154 average time/residue: 0.1113 time to fit residues: 24.7884 Evaluate side-chains 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 22 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.178118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146642 restraints weight = 16366.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146032 restraints weight = 18221.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148919 restraints weight = 15629.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148247 restraints weight = 11477.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148509 restraints weight = 11534.345| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12302 Z= 0.119 Angle : 0.626 13.006 16822 Z= 0.322 Chirality : 0.042 0.232 1828 Planarity : 0.004 0.061 1925 Dihedral : 19.252 133.198 2199 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.75 % Allowed : 18.21 % Favored : 79.04 % 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 aren not related in a simple way. whole: -2.68 (0.23), residues: 1272 helix: -1.65 (0.22), residues: 513 sheet: -1.46 (0.56), residues: 97 loop : -1.90 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.015 0.001 TYR A 11 PHE 0.027 0.001 PHE A 888 TRP 0.021 0.002 TRP A1163 HIS 0.009 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00267 (12302) covalent geometry : angle 0.62595 (16822) hydrogen bonds : bond 0.05121 ( 235) hydrogen bonds : angle 4.62605 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.5898 (mp0) cc_final: 0.5427 (tt0) REVERT: A 274 ASN cc_start: 0.7425 (p0) cc_final: 0.7183 (p0) REVERT: A 311 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6584 (mp) REVERT: A 345 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6134 (t0) REVERT: A 570 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: A 689 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7584 (tp) REVERT: A 785 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6959 (tt) REVERT: A 789 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7326 (p90) REVERT: A 964 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.5563 (ppt170) REVERT: A 1066 LYS cc_start: 0.7331 (mtpm) cc_final: 0.6806 (mptt) outliers start: 32 outliers final: 19 residues processed: 152 average time/residue: 0.1112 time to fit residues: 24.3308 Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.174084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142637 restraints weight = 16950.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142793 restraints weight = 19517.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143877 restraints weight = 17448.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144277 restraints weight = 13489.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144733 restraints weight = 13696.796| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12302 Z= 0.167 Angle : 0.679 18.309 16822 Z= 0.348 Chirality : 0.044 0.228 1828 Planarity : 0.004 0.061 1925 Dihedral : 19.371 137.078 2199 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.41 % Allowed : 18.90 % Favored : 78.69 % 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 aren not related in a simple way. whole: -2.74 (0.23), residues: 1272 helix: -1.61 (0.22), residues: 511 sheet: -1.56 (0.56), residues: 97 loop : -2.01 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.017 0.001 TYR A 11 PHE 0.027 0.002 PHE A 888 TRP 0.021 0.002 TRP A1163 HIS 0.011 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00387 (12302) covalent geometry : angle 0.67945 (16822) hydrogen bonds : bond 0.04643 ( 235) hydrogen bonds : angle 4.67693 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7516 (p0) cc_final: 0.7282 (p0) REVERT: A 311 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6366 (mp) REVERT: A 345 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6633 (t0) REVERT: A 570 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: A 689 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7550 (tp) REVERT: A 785 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6965 (tt) REVERT: A 789 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7354 (p90) REVERT: A 964 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5510 (ppt170) REVERT: A 980 MET cc_start: 0.7728 (tmm) cc_final: 0.7504 (tmm) REVERT: A 1066 LYS cc_start: 0.7356 (mtpm) cc_final: 0.6817 (mptt) outliers start: 28 outliers final: 20 residues processed: 152 average time/residue: 0.1236 time to fit residues: 27.2467 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.0030 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145287 restraints weight = 16752.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145684 restraints weight = 18276.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147150 restraints weight = 16793.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147198 restraints weight = 14322.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147723 restraints weight = 13651.100| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12302 Z= 0.136 Angle : 0.657 18.038 16822 Z= 0.336 Chirality : 0.042 0.224 1828 Planarity : 0.003 0.063 1925 Dihedral : 19.354 140.118 2199 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.58 % Allowed : 19.16 % Favored : 78.26 % 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 aren not related in a simple way. whole: -2.67 (0.23), residues: 1272 helix: -1.55 (0.22), residues: 515 sheet: -1.50 (0.57), residues: 97 loop : -1.98 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.016 0.001 TYR A 11 PHE 0.025 0.001 PHE A 888 TRP 0.021 0.002 TRP A1163 HIS 0.010 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00311 (12302) covalent geometry : angle 0.65694 (16822) hydrogen bonds : bond 0.04908 ( 235) hydrogen bonds : angle 4.61750 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.75 seconds wall clock time: 33 minutes 15.30 seconds (1995.30 seconds total)