Starting phenix.real_space_refine on Tue Jun 10 21:08:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtc_0061/06_2025/6gtc_0061.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtc_0061/06_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_0061/06_2025/6gtc_0061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtc_0061/06_2025/6gtc_0061.map" model { file = "/net/cci-nas-00/data/ceres_data/6gtc_0061/06_2025/6gtc_0061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtc_0061/06_2025/6gtc_0061.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.03, per 1000 atoms: 0.59 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.95 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: 4.62 Time building geometry restraints manager: 3.19 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.003 TRP A 971 HIS 0.008 0.002 HIS A 544 PHE 0.027 0.002 PHE A 258 TYR 0.021 0.002 TYR A 272 ARG 0.007 0.000 ARG A 833 Details of bonding type rmsd hydrogen bonds : bond 0.34175 ( 235) hydrogen bonds : angle 11.30654 ( 657) covalent geometry : bond 0.00425 (12302) covalent geometry : angle 0.94475 (16822) *********************** 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 : 1.128 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: 0.6608 (mm) REVERT: A 920 GLU cc_start: 0.4849 (mt-10) cc_final: 0.4204 (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: 0.2778 time to fit residues: 102.5952 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 : 1.235 ------------------------------------------------------------------------------- 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 112 optimal weight: 0.0570 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 126 ASN A 305 ASN A 395 ASN A 538 HIS A 588 GLN A 612 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 843 HIS A 851 ASN A 853 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149387 restraints weight = 16253.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.148343 restraints weight = 18592.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149546 restraints weight = 15273.274| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12302 Z= 0.142 Angle : 0.674 12.514 16822 Z= 0.362 Chirality : 0.043 0.240 1828 Planarity : 0.005 0.078 1925 Dihedral : 19.034 128.051 2201 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.66 % Allowed : 11.94 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.18), residues: 1272 helix: -3.73 (0.15), residues: 513 sheet: -2.52 (0.48), residues: 107 loop : -2.97 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 971 HIS 0.007 0.001 HIS A 990 PHE 0.017 0.002 PHE A1108 TYR 0.016 0.002 TYR A 11 ARG 0.006 0.001 ARG A1166 Details of bonding type rmsd hydrogen bonds : bond 0.06579 ( 235) hydrogen bonds : angle 6.43109 ( 657) covalent geometry : bond 0.00308 (12302) covalent geometry : angle 0.67386 (16822) *********************** 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 200 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6448 (mtmt) cc_final: 0.6164 (mtmt) REVERT: A 294 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7842 (t0) REVERT: A 311 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6542 (mp) REVERT: A 352 MET cc_start: 0.6699 (ttm) cc_final: 0.6380 (ttm) REVERT: A 688 ILE cc_start: 0.7522 (mp) cc_final: 0.7262 (mt) REVERT: A 980 MET cc_start: 0.7746 (tmm) cc_final: 0.7529 (tmm) REVERT: A 1099 TYR cc_start: 0.4739 (t80) cc_final: 0.4516 (t80) REVERT: A 1221 LYS cc_start: 0.5929 (tptp) cc_final: 0.5659 (tptp) outliers start: 31 outliers final: 16 residues processed: 192 average time/residue: 0.2463 time to fit residues: 67.6985 Evaluate side-chains 163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 890 SER Chi-restraints excluded: chain A residue 915 SER 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 1151 LEU 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 103 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 538 HIS A 580 ASN A 602 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.169068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137215 restraints weight = 17153.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.136606 restraints weight = 21209.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138996 restraints weight = 18795.852| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12302 Z= 0.258 Angle : 0.787 18.552 16822 Z= 0.407 Chirality : 0.047 0.204 1828 Planarity : 0.005 0.073 1925 Dihedral : 19.290 131.207 2199 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.04 % Allowed : 13.49 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.20), residues: 1272 helix: -3.10 (0.18), residues: 489 sheet: -2.60 (0.53), residues: 96 loop : -2.61 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.007 0.001 HIS A 990 PHE 0.028 0.003 PHE A 622 TYR 0.025 0.002 TYR A 47 ARG 0.006 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 235) hydrogen bonds : angle 6.09522 ( 657) covalent geometry : bond 0.00594 (12302) covalent geometry : angle 0.78656 (16822) *********************** 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 202 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.264 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 51 LYS cc_start: 0.6821 (mtmt) cc_final: 0.6600 (ttmt) REVERT: A 180 LYS cc_start: 0.7423 (ttmm) cc_final: 0.7222 (ttmm) REVERT: A 646 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6693 (mt) REVERT: A 783 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 785 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7116 (tt) REVERT: A 789 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 888 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7257 (t80) outliers start: 47 outliers final: 28 residues processed: 188 average time/residue: 0.2623 time to fit residues: 69.8867 Evaluate side-chains 169 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 279 THR 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 627 LYS Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 783 LEU 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 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 941 PHE Chi-restraints excluded: chain A residue 944 ILE 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 1035 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** A 912 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.173189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140652 restraints weight = 16722.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140312 restraints weight = 19357.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143004 restraints weight = 17682.727| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12302 Z= 0.144 Angle : 0.662 14.705 16822 Z= 0.346 Chirality : 0.043 0.193 1828 Planarity : 0.004 0.071 1925 Dihedral : 19.182 132.504 2199 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.95 % Allowed : 16.15 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.21), residues: 1272 helix: -2.68 (0.20), residues: 504 sheet: -2.25 (0.54), residues: 95 loop : -2.36 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 609 HIS 0.005 0.001 HIS A 990 PHE 0.024 0.002 PHE A1108 TYR 0.022 0.001 TYR A 47 ARG 0.004 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 235) hydrogen bonds : angle 5.56513 ( 657) covalent geometry : bond 0.00327 (12302) covalent geometry : angle 0.66220 (16822) *********************** 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 190 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.302 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: symmetry clash REVERT: A 43 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7198 (ttp-110) REVERT: A 51 LYS cc_start: 0.6723 (mtmt) cc_final: 0.6454 (ttmt) REVERT: A 83 TYR cc_start: 0.7152 (t80) cc_final: 0.6894 (t80) REVERT: A 180 LYS cc_start: 0.7316 (ttmm) cc_final: 0.7106 (ttmm) REVERT: A 311 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 570 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: A 789 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7320 (p90) outliers start: 46 outliers final: 24 residues processed: 174 average time/residue: 0.2864 time to fit residues: 73.5330 Evaluate side-chains 162 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 TYR 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 487 MET 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 657 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 789 TYR 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 890 SER 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 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 0.0870 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 HIS ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139887 restraints weight = 16813.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139762 restraints weight = 21018.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141955 restraints weight = 18403.025| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12302 Z= 0.154 Angle : 0.657 12.934 16822 Z= 0.342 Chirality : 0.043 0.188 1828 Planarity : 0.004 0.069 1925 Dihedral : 19.159 132.928 2199 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.30 % Allowed : 16.32 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.22), residues: 1272 helix: -2.44 (0.20), residues: 513 sheet: -2.00 (0.56), residues: 95 loop : -2.26 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1163 HIS 0.004 0.001 HIS A 544 PHE 0.018 0.002 PHE A 888 TYR 0.021 0.001 TYR A 47 ARG 0.004 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 235) hydrogen bonds : angle 5.30686 ( 657) covalent geometry : bond 0.00350 (12302) covalent geometry : angle 0.65679 (16822) *********************** 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 191 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: A 43 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7286 (ttp-110) REVERT: A 51 LYS cc_start: 0.6736 (mtmt) cc_final: 0.6443 (ttmt) REVERT: A 311 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 570 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: A 689 LEU cc_start: 0.8054 (mm) cc_final: 0.7630 (tp) REVERT: A 785 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7101 (tt) REVERT: A 789 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7299 (p90) REVERT: A 856 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7685 (p0) REVERT: A 943 ILE cc_start: 0.6502 (mm) cc_final: 0.6240 (mt) REVERT: A 964 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.5594 (ppt170) outliers start: 50 outliers final: 27 residues processed: 174 average time/residue: 0.2541 time to fit residues: 63.8218 Evaluate side-chains 170 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 487 MET 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 627 LYS Chi-restraints excluded: chain A residue 657 ILE 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 856 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS 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 941 PHE 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 1052 LEU 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 1237 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 104 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 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 = 0.4215 r_free = 0.4215 target = 0.174879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143720 restraints weight = 16879.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143717 restraints weight = 21020.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144803 restraints weight = 18259.435| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12302 Z= 0.127 Angle : 0.623 13.155 16822 Z= 0.326 Chirality : 0.042 0.177 1828 Planarity : 0.004 0.067 1925 Dihedral : 19.160 132.769 2199 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.69 % Allowed : 17.10 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.22), residues: 1272 helix: -2.16 (0.21), residues: 509 sheet: -1.66 (0.59), residues: 95 loop : -2.17 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1163 HIS 0.003 0.001 HIS A 544 PHE 0.018 0.001 PHE A 888 TYR 0.021 0.001 TYR A 47 ARG 0.004 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 235) hydrogen bonds : angle 5.00961 ( 657) covalent geometry : bond 0.00284 (12302) covalent geometry : angle 0.62288 (16822) *********************** 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 185 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.296 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 20 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: A 285 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7444 (tt) REVERT: A 311 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6727 (mp) REVERT: A 401 ASP cc_start: 0.6939 (t70) cc_final: 0.6600 (m-30) REVERT: A 570 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6366 (m-80) REVERT: A 689 LEU cc_start: 0.8050 (mm) cc_final: 0.7639 (tp) REVERT: A 785 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7092 (tt) REVERT: A 789 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7347 (p90) REVERT: A 943 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6271 (mt) REVERT: A 964 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.5616 (ppt170) outliers start: 43 outliers final: 24 residues processed: 170 average time/residue: 0.2415 time to fit residues: 59.6503 Evaluate side-chains 162 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU 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 279 THR Chi-restraints excluded: chain A residue 285 ILE 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 487 MET 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 657 ILE 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 829 GLU Chi-restraints excluded: chain A residue 882 CYS 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 943 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 129 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** 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 = 0.4165 r_free = 0.4165 target = 0.170260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139159 restraints weight = 17106.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138911 restraints weight = 19514.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141186 restraints weight = 18030.232| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12302 Z= 0.197 Angle : 0.689 11.337 16822 Z= 0.359 Chirality : 0.045 0.180 1828 Planarity : 0.005 0.079 1925 Dihedral : 19.307 133.022 2199 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 4.12 % Allowed : 17.01 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.22), residues: 1272 helix: -2.14 (0.21), residues: 513 sheet: -1.71 (0.58), residues: 97 loop : -2.17 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1163 HIS 0.008 0.001 HIS A 990 PHE 0.025 0.002 PHE A 710 TYR 0.023 0.002 TYR A 11 ARG 0.004 0.001 ARG A 833 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 235) hydrogen bonds : angle 5.10699 ( 657) covalent geometry : bond 0.00457 (12302) covalent geometry : angle 0.68923 (16822) *********************** 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 186 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 43 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6603 (ttp-110) REVERT: A 274 ASN cc_start: 0.7416 (p0) cc_final: 0.7152 (p0) REVERT: A 311 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6717 (mp) REVERT: A 785 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7063 (tt) REVERT: A 789 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7448 (p90) REVERT: A 964 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.5650 (ppt170) REVERT: A 995 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7491 (mm) REVERT: A 1023 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8406 (t) outliers start: 48 outliers final: 33 residues processed: 169 average time/residue: 0.2491 time to fit residues: 61.8957 Evaluate side-chains 173 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 ARG 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 177 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 487 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 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 882 CYS 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 995 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1052 LEU 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 1217 MET Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144726 restraints weight = 16897.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144040 restraints weight = 20940.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146096 restraints weight = 18228.830| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12302 Z= 0.125 Angle : 0.638 11.626 16822 Z= 0.329 Chirality : 0.042 0.208 1828 Planarity : 0.004 0.066 1925 Dihedral : 19.267 133.272 2199 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.35 % Allowed : 18.13 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.22), residues: 1272 helix: -1.96 (0.22), residues: 513 sheet: -0.60 (0.70), residues: 73 loop : -2.14 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 609 HIS 0.008 0.001 HIS A 990 PHE 0.026 0.001 PHE A 888 TYR 0.020 0.001 TYR A 47 ARG 0.003 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 235) hydrogen bonds : angle 4.87934 ( 657) covalent geometry : bond 0.00280 (12302) covalent geometry : angle 0.63831 (16822) *********************** 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 181 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.5378 (m-10) REVERT: A 274 ASN cc_start: 0.7408 (p0) cc_final: 0.7203 (p0) REVERT: A 311 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6745 (mp) REVERT: A 345 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6062 (t0) REVERT: A 689 LEU cc_start: 0.7989 (mm) cc_final: 0.7522 (tp) REVERT: A 785 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7057 (tt) REVERT: A 789 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7349 (p90) REVERT: A 964 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5672 (ppt170) REVERT: A 995 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7305 (mm) outliers start: 39 outliers final: 24 residues processed: 169 average time/residue: 0.2405 time to fit residues: 58.9242 Evaluate side-chains 162 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 279 THR 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 487 MET Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 657 ILE 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 868 ILE 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1058 THR 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 1217 MET Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 74 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147574 restraints weight = 16589.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147519 restraints weight = 21126.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149556 restraints weight = 17675.564| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4496 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= 0.118 Angle : 0.633 15.058 16822 Z= 0.327 Chirality : 0.042 0.218 1828 Planarity : 0.004 0.064 1925 Dihedral : 19.298 133.639 2199 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.49 % Allowed : 19.50 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.22), residues: 1272 helix: -1.83 (0.22), residues: 517 sheet: -0.63 (0.69), residues: 73 loop : -2.05 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 609 HIS 0.005 0.001 HIS A 954 PHE 0.025 0.001 PHE A 888 TYR 0.020 0.001 TYR A 11 ARG 0.006 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 235) hydrogen bonds : angle 4.73853 ( 657) covalent geometry : bond 0.00257 (12302) covalent geometry : angle 0.63285 (16822) *********************** 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 174 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7384 (p0) cc_final: 0.7164 (p0) REVERT: A 311 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6694 (mp) REVERT: A 345 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.5830 (t0) REVERT: A 689 LEU cc_start: 0.7977 (mm) cc_final: 0.7548 (tp) REVERT: A 789 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7375 (p90) REVERT: A 964 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5710 (ppt170) REVERT: A 995 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7209 (mm) REVERT: A 1066 LYS cc_start: 0.7310 (mtpm) cc_final: 0.6830 (mptt) REVERT: A 1244 ARG cc_start: 0.6695 (mpp80) cc_final: 0.5859 (mtm-85) outliers start: 29 outliers final: 20 residues processed: 162 average time/residue: 0.2487 time to fit residues: 58.1046 Evaluate side-chains 159 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 487 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 657 ILE Chi-restraints excluded: chain A residue 724 TYR 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1217 MET Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 0.0050 chunk 38 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 602 ASN A 760 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148914 restraints weight = 16533.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148557 restraints weight = 19230.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150948 restraints weight = 16993.050| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4611 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= 0.116 Angle : 0.635 14.108 16822 Z= 0.325 Chirality : 0.042 0.225 1828 Planarity : 0.003 0.065 1925 Dihedral : 19.311 133.640 2199 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.41 % Allowed : 19.50 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1272 helix: -1.70 (0.22), residues: 521 sheet: -0.72 (0.69), residues: 73 loop : -2.00 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 609 HIS 0.008 0.001 HIS A 990 PHE 0.022 0.001 PHE A1128 TYR 0.019 0.001 TYR A 47 ARG 0.005 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 235) hydrogen bonds : angle 4.63826 ( 657) covalent geometry : bond 0.00255 (12302) covalent geometry : angle 0.63491 (16822) ********************** 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 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.5472 (m-10) REVERT: A 274 ASN cc_start: 0.7384 (p0) cc_final: 0.7168 (p0) REVERT: A 311 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6667 (mp) REVERT: A 345 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.5592 (t0) REVERT: A 689 LEU cc_start: 0.7961 (mm) cc_final: 0.7556 (tp) REVERT: A 964 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5660 (ppt170) REVERT: A 1066 LYS cc_start: 0.7249 (mtpm) cc_final: 0.6848 (mptt) REVERT: A 1244 ARG cc_start: 0.6704 (mpp80) cc_final: 0.5856 (mtm-85) outliers start: 28 outliers final: 18 residues processed: 153 average time/residue: 0.2540 time to fit residues: 56.2954 Evaluate side-chains 154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 724 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1058 THR 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 1295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.177484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145616 restraints weight = 16610.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145460 restraints weight = 19545.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147597 restraints weight = 17215.260| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12302 Z= 0.126 Angle : 0.633 13.946 16822 Z= 0.327 Chirality : 0.042 0.229 1828 Planarity : 0.003 0.063 1925 Dihedral : 19.327 133.780 2199 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.15 % Allowed : 19.76 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.23), residues: 1272 helix: -1.57 (0.22), residues: 518 sheet: -0.94 (0.65), residues: 85 loop : -2.01 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 141 HIS 0.007 0.001 HIS A 990 PHE 0.021 0.001 PHE A 888 TYR 0.021 0.001 TYR A 11 ARG 0.004 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 235) hydrogen bonds : angle 4.65321 ( 657) covalent geometry : bond 0.00285 (12302) covalent geometry : angle 0.63337 (16822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.96 seconds wall clock time: 68 minutes 24.87 seconds (4104.87 seconds total)