Starting phenix.real_space_refine on Thu Mar 5 12:55:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.map" model { file = "/net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8q_14560/03_2026/7z8q_14560.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 84 5.16 5 C 14091 2.51 5 N 3986 2.21 5 O 4321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22485 Number of models: 1 Model: "" Number of chains: 6 Chain: "a" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1700 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "b" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1749 Classifications: {'peptide': 230} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 215} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8453 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1027} Chain breaks: 1 Chain: "d" Number of atoms: 9939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9939 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1207} Chain breaks: 1 Chain: "e" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 74} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18958 SG CYS d 891 51.768 110.988 122.111 1.00 41.50 S ATOM 19532 SG CYS d 968 52.838 107.395 120.371 1.00 46.68 S ATOM 19574 SG CYS d 975 53.380 108.718 123.987 1.00 39.55 S ATOM 19592 SG CYS d 978 50.125 107.764 123.191 1.00 42.32 S ATOM 12378 SG CYS d 60 110.765 80.223 101.698 1.00112.36 S ATOM 12396 SG CYS d 62 112.453 80.038 98.849 1.00113.61 S ATOM 12505 SG CYS d 75 111.831 83.602 99.229 1.00114.67 S ATOM 12531 SG CYS d 78 109.306 81.717 98.326 1.00112.81 S Time building chain proxies: 4.96, per 1000 atoms: 0.22 Number of scatterers: 22485 At special positions: 0 Unit cell: (125.4, 133.1, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 84 16.00 Mg 1 11.99 O 4321 8.00 N 3986 7.00 C 14091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " Number of angles added : 12 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5314 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 40 sheets defined 39.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.913A pdb=" N SER a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 110 No H-bonds generated for 'chain 'a' and resid 108 through 110' Processing helix chain 'a' and resid 148 through 153 Processing helix chain 'a' and resid 203 through 224 removed outlier: 3.533A pdb=" N ALA a 207 " --> pdb=" O SER a 203 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG a 223 " --> pdb=" O PHE a 219 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU a 224 " --> pdb=" O GLY a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 4.022A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 Processing helix chain 'b' and resid 108 through 110 No H-bonds generated for 'chain 'b' and resid 108 through 110' Processing helix chain 'b' and resid 148 through 153 Processing helix chain 'b' and resid 203 through 225 removed outlier: 4.024A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.951A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.568A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 256 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 removed outlier: 3.757A pdb=" N GLU c 297 " --> pdb=" O GLN c 293 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 321 Processing helix chain 'c' and resid 334 through 351 Processing helix chain 'c' and resid 380 through 407 removed outlier: 3.510A pdb=" N LEU c 384 " --> pdb=" O THR c 380 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL c 399 " --> pdb=" O ARG c 395 " (cutoff:3.500A) Processing helix chain 'c' and resid 413 through 418 Processing helix chain 'c' and resid 420 through 434 Processing helix chain 'c' and resid 444 through 453 Processing helix chain 'c' and resid 470 through 474 Processing helix chain 'c' and resid 532 through 538 Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.540A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 601 through 613 removed outlier: 3.843A pdb=" N ARG c 613 " --> pdb=" O ALA c 609 " (cutoff:3.500A) Processing helix chain 'c' and resid 631 through 637 Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.108A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 removed outlier: 3.581A pdb=" N LEU c 932 " --> pdb=" O ILE c 928 " (cutoff:3.500A) Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.660A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 removed outlier: 3.537A pdb=" N CYS c1073 " --> pdb=" O GLY c1069 " (cutoff:3.500A) Processing helix chain 'c' and resid 1082 through 1091 Processing helix chain 'c' and resid 1095 through 1108 Processing helix chain 'c' and resid 1118 through 1129 Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 84 through 91 removed outlier: 4.084A pdb=" N ARG d 91 " --> pdb=" O ARG d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.856A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS d 108 " --> pdb=" O ILE d 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 103 through 108' Processing helix chain 'd' and resid 112 through 119 Processing helix chain 'd' and resid 121 through 131 Processing helix chain 'd' and resid 140 through 146 removed outlier: 3.729A pdb=" N ARG d 144 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 188 Processing helix chain 'd' and resid 190 through 228 Processing helix chain 'd' and resid 237 through 248 removed outlier: 3.551A pdb=" N TYR d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 258 through 268 Processing helix chain 'd' and resid 270 through 283 Processing helix chain 'd' and resid 285 through 306 removed outlier: 4.151A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.583A pdb=" N GLY d 311 " --> pdb=" O SER d 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 308 through 311' Processing helix chain 'd' and resid 339 through 361 Processing helix chain 'd' and resid 363 through 383 removed outlier: 3.711A pdb=" N VAL d 367 " --> pdb=" O PRO d 363 " (cutoff:3.500A) Processing helix chain 'd' and resid 401 through 406 Processing helix chain 'd' and resid 411 through 416 Processing helix chain 'd' and resid 445 through 452 removed outlier: 4.084A pdb=" N GLU d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 483 through 491 removed outlier: 3.650A pdb=" N ILE d 491 " --> pdb=" O LEU d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 505 through 507 No H-bonds generated for 'chain 'd' and resid 505 through 507' Processing helix chain 'd' and resid 525 through 527 No H-bonds generated for 'chain 'd' and resid 525 through 527' Processing helix chain 'd' and resid 528 through 533 Processing helix chain 'd' and resid 548 through 558 removed outlier: 3.863A pdb=" N ALA d 553 " --> pdb=" O ALA d 549 " (cutoff:3.500A) Processing helix chain 'd' and resid 580 through 590 Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 4.183A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 668 through 675 Processing helix chain 'd' and resid 689 through 704 Processing helix chain 'd' and resid 705 through 725 removed outlier: 4.022A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) Processing helix chain 'd' and resid 726 through 728 No H-bonds generated for 'chain 'd' and resid 726 through 728' Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.621A pdb=" N ILE d 745 " --> pdb=" O ARG d 741 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 Processing helix chain 'd' and resid 810 through 819 removed outlier: 3.824A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.590A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA d 868 " --> pdb=" O ALA d 864 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER d 881 " --> pdb=" O LEU d 877 " (cutoff:3.500A) Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 975 through 980 Processing helix chain 'd' and resid 995 through 1005 Processing helix chain 'd' and resid 1006 through 1010 Processing helix chain 'd' and resid 1027 through 1037 removed outlier: 3.505A pdb=" N VAL d1031 " --> pdb=" O GLY d1027 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.988A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.139A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1183 through 1196 Processing helix chain 'd' and resid 1209 through 1216 removed outlier: 3.757A pdb=" N ALA d1216 " --> pdb=" O LYS d1212 " (cutoff:3.500A) Processing helix chain 'd' and resid 1219 through 1227 Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1248 through 1255 Processing helix chain 'd' and resid 1260 through 1263 Processing helix chain 'd' and resid 1264 through 1269 removed outlier: 3.811A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1281 Processing helix chain 'e' and resid 39 through 47 removed outlier: 4.169A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG e 46 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 70 removed outlier: 3.607A pdb=" N VAL e 54 " --> pdb=" O LYS e 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 100 Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 13 removed outlier: 3.689A pdb=" N LEU a 9 " --> pdb=" O GLU a 24 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU a 24 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE a 189 " --> pdb=" O THR a 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 173 " --> pdb=" O GLU a 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 3.660A pdb=" N LEU a 138 " --> pdb=" O MET a 95 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER a 53 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU a 141 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL a 51 " --> pdb=" O GLU a 141 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY a 143 " --> pdb=" O ALA a 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA a 49 " --> pdb=" O GLY a 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.577A pdb=" N SER a 86 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR a 117 " --> pdb=" O SER a 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 removed outlier: 3.556A pdb=" N GLY a 103 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU a 128 " --> pdb=" O GLY a 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA a 126 " --> pdb=" O VAL a 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.681A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.681A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE b 193 " --> pdb=" O LYS b 177 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS b 173 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 93 through 97 removed outlier: 6.264A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE b 54 " --> pdb=" O ILE b 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE b 162 " --> pdb=" O ILE b 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 97 removed outlier: 3.960A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'b' and resid 103 through 106 removed outlier: 4.144A pdb=" N ALA b 126 " --> pdb=" O VAL b 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 96 through 97 removed outlier: 4.760A pdb=" N LEU c 105 " --> pdb=" O ILE c 140 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE c 140 " --> pdb=" O LEU c 105 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE c 107 " --> pdb=" O GLU c 138 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU c 138 " --> pdb=" O PHE c 107 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP c 109 " --> pdb=" O THR c 136 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR c 136 " --> pdb=" O ASP c 109 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 166 through 168 removed outlier: 3.541A pdb=" N GLN c 438 " --> pdb=" O VAL c 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.577A pdb=" N GLN c 178 " --> pdb=" O ARG c 379 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER c 177 " --> pdb=" O SER c 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU c 455 " --> pdb=" O GLY c 498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 184 through 191 Processing sheet with id=AB6, first strand: chain 'c' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'c' and resid 354 through 355 removed outlier: 3.612A pdb=" N VAL c 363 " --> pdb=" O MET c 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'c' and resid 667 through 671 removed outlier: 6.944A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 687 through 688 removed outlier: 3.668A pdb=" N ASP c 704 " --> pdb=" O CYS c 687 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.128A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE c 735 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE c 898 " --> pdb=" O ILE c 735 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU c 737 " --> pdb=" O ILE c 898 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.128A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 748 through 752 removed outlier: 6.737A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 748 through 752 removed outlier: 4.046A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 768 through 769 removed outlier: 3.911A pdb=" N GLU c 768 " --> pdb=" O VAL c 806 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.965A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.774A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET d 541 " --> pdb=" O SER d 428 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU d 498 " --> pdb=" O GLN d 510 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN d 510 " --> pdb=" O LEU d 498 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 7.546A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 1133 through 1135 Processing sheet with id=AD2, first strand: chain 'd' and resid 9 through 10 Processing sheet with id=AD3, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AD4, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD5, first strand: chain 'd' and resid 134 through 135 removed outlier: 3.645A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.453A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.580A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 637 " --> pdb=" O TRP d 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP d 662 " --> pdb=" O LEU d 637 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.580A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.791A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 902 through 903 Processing sheet with id=AE2, first strand: chain 'd' and resid 1051 through 1056 removed outlier: 3.938A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 1181 through 1182 removed outlier: 3.723A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 1272 through 1274 917 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7755 1.34 - 1.46: 4452 1.46 - 1.58: 10515 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 22869 Sorted by residual: bond pdb=" N ILE e 75 " pdb=" CA ILE e 75 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.24e-02 6.50e+03 1.23e+01 bond pdb=" N GLY d 257 " pdb=" CA GLY d 257 " ideal model delta sigma weight residual 1.449 1.480 -0.032 1.00e-02 1.00e+04 1.00e+01 bond pdb=" N ARG d1060 " pdb=" CA ARG d1060 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 9.87e+00 bond pdb=" N GLU d 259 " pdb=" CA GLU d 259 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.29e+00 bond pdb=" N ILE d 129 " pdb=" CA ILE d 129 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 8.88e+00 ... (remaining 22864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 30418 1.56 - 3.11: 401 3.11 - 4.67: 154 4.67 - 6.23: 8 6.23 - 7.78: 3 Bond angle restraints: 30984 Sorted by residual: angle pdb=" N GLU e 77 " pdb=" CA GLU e 77 " pdb=" C GLU e 77 " ideal model delta sigma weight residual 114.04 106.26 7.78 1.24e+00 6.50e-01 3.94e+01 angle pdb=" CA GLY d 257 " pdb=" C GLY d 257 " pdb=" O GLY d 257 " ideal model delta sigma weight residual 122.33 118.18 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA THR d 893 " pdb=" C THR d 893 " pdb=" O THR d 893 " ideal model delta sigma weight residual 121.89 116.73 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" C ASN e 69 " pdb=" N GLN e 70 " pdb=" CA GLN e 70 " ideal model delta sigma weight residual 122.27 115.02 7.25 1.85e+00 2.92e-01 1.54e+01 angle pdb=" CA CYS d 968 " pdb=" C CYS d 968 " pdb=" O CYS d 968 " ideal model delta sigma weight residual 121.19 116.94 4.25 1.10e+00 8.26e-01 1.49e+01 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13380 17.95 - 35.89: 558 35.89 - 53.84: 67 53.84 - 71.78: 17 71.78 - 89.73: 5 Dihedral angle restraints: 14027 sinusoidal: 5758 harmonic: 8269 Sorted by residual: dihedral pdb=" CA GLY d 257 " pdb=" C GLY d 257 " pdb=" N ALA d 258 " pdb=" CA ALA d 258 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO d 577 " pdb=" C PRO d 577 " pdb=" N ARG d 578 " pdb=" CA ARG d 578 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN d 882 " pdb=" C GLN d 882 " pdb=" N ASP d 883 " pdb=" CA ASP d 883 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2973 0.053 - 0.105: 416 0.105 - 0.158: 124 0.158 - 0.211: 6 0.211 - 0.263: 4 Chirality restraints: 3523 Sorted by residual: chirality pdb=" CA ILE e 75 " pdb=" N ILE e 75 " pdb=" C ILE e 75 " pdb=" CB ILE e 75 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR e 107 " pdb=" N THR e 107 " pdb=" C THR e 107 " pdb=" CB THR e 107 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PHE d 131 " pdb=" N PHE d 131 " pdb=" C PHE d 131 " pdb=" CB PHE d 131 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3520 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET d 256 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C MET d 256 " -0.065 2.00e-02 2.50e+03 pdb=" O MET d 256 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY d 257 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 128 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ILE d 128 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE d 128 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE d 129 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN d 352 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C ASN d 352 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN d 352 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG d 353 " -0.017 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.17: 20414 3.17 - 3.74: 32333 3.74 - 4.32: 43508 4.32 - 4.90: 73493 Nonbonded interactions: 169976 Sorted by model distance: nonbonded pdb=" OH TYR d 241 " pdb=" O GLY d 254 " model vdw 2.012 3.040 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASP d 539 " pdb="MG MG d1503 " model vdw 2.067 2.170 nonbonded pdb=" OD1 ASP d 537 " pdb="MG MG d1503 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASP d 535 " pdb="MG MG d1503 " model vdw 2.072 2.170 ... (remaining 169971 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 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 4 through 210 or (resid 211 through 212 and (name N or nam \ e CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 4 through 226) } 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: 2.820 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.810 Find NCS groups from input model: 0.230 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22877 Z= 0.164 Angle : 0.589 30.845 30996 Z= 0.301 Chirality : 0.043 0.263 3523 Planarity : 0.003 0.048 4096 Dihedral : 9.984 89.730 8713 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 0.37 % Allowed : 4.05 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2877 helix: 1.32 (0.17), residues: 1006 sheet: -1.43 (0.29), residues: 324 loop : -1.17 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d1143 TYR 0.013 0.001 TYR e 56 PHE 0.009 0.001 PHE c 139 TRP 0.005 0.001 TRP d 778 HIS 0.002 0.000 HIS d 439 Details of bonding type rmsd covalent geometry : bond 0.00262 (22869) covalent geometry : angle 0.51622 (30984) hydrogen bonds : bond 0.19907 ( 897) hydrogen bonds : angle 6.91981 ( 2577) metal coordination : bond 0.02508 ( 8) metal coordination : angle 14.40884 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 612 time to evaluate : 0.991 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 168 TYR cc_start: 0.7617 (m-80) cc_final: 0.7282 (m-80) REVERT: b 61 HIS cc_start: 0.6337 (m-70) cc_final: 0.6136 (m90) REVERT: c 444 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8017 (p0) REVERT: c 591 THR cc_start: 0.8834 (p) cc_final: 0.8056 (t) REVERT: c 612 GLN cc_start: 0.7961 (mt0) cc_final: 0.7323 (tp40) REVERT: d 736 VAL cc_start: 0.8530 (t) cc_final: 0.8321 (m) REVERT: d 816 THR cc_start: 0.9092 (m) cc_final: 0.8881 (p) REVERT: d 966 LEU cc_start: 0.6138 (tp) cc_final: 0.5591 (tt) outliers start: 9 outliers final: 0 residues processed: 620 average time/residue: 0.1807 time to fit residues: 164.7562 Evaluate side-chains 303 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 185 GLN c 298 ASN c 610 ASN c 889 HIS ** c1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 341 ASN ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN d 797 ASN ** d 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1145 GLN e 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.090406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067663 restraints weight = 97470.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069553 restraints weight = 55294.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070813 restraints weight = 37765.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071644 restraints weight = 29014.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072110 restraints weight = 24396.034| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22877 Z= 0.241 Angle : 0.716 13.463 30996 Z= 0.361 Chirality : 0.046 0.268 3523 Planarity : 0.005 0.053 4096 Dihedral : 4.277 21.653 3171 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2877 helix: 0.93 (0.16), residues: 1033 sheet: -1.26 (0.28), residues: 356 loop : -1.10 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 218 TYR 0.020 0.002 TYR b 32 PHE 0.017 0.002 PHE c 252 TRP 0.013 0.001 TRP c1074 HIS 0.005 0.001 HIS e 100 Details of bonding type rmsd covalent geometry : bond 0.00532 (22869) covalent geometry : angle 0.70193 (30984) hydrogen bonds : bond 0.05120 ( 897) hydrogen bonds : angle 5.38296 ( 2577) metal coordination : bond 0.02696 ( 8) metal coordination : angle 7.31525 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 0.917 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 103 MET cc_start: 0.4803 (tpt) cc_final: 0.4402 (tpt) REVERT: c 195 THR cc_start: 0.7500 (m) cc_final: 0.7077 (m) REVERT: c 243 TRP cc_start: 0.7481 (t-100) cc_final: 0.7179 (t-100) REVERT: c 393 MET cc_start: 0.8484 (ttm) cc_final: 0.8014 (ttp) REVERT: c 396 MET cc_start: 0.8366 (tmm) cc_final: 0.8132 (tmm) REVERT: c 513 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7402 (mm-30) REVERT: c 612 GLN cc_start: 0.8141 (mt0) cc_final: 0.7794 (mt0) REVERT: c 724 MET cc_start: 0.8420 (ppp) cc_final: 0.7751 (ppp) REVERT: c 883 ASP cc_start: 0.7584 (m-30) cc_final: 0.7116 (m-30) REVERT: c 926 MET cc_start: 0.8841 (tpp) cc_final: 0.8548 (tpt) REVERT: c 1077 GLN cc_start: 0.9111 (mt0) cc_final: 0.8898 (mt0) REVERT: c 1119 GLU cc_start: 0.7356 (mp0) cc_final: 0.6841 (mp0) REVERT: d 92 MET cc_start: 0.8112 (mmp) cc_final: 0.6463 (mmp) REVERT: d 142 GLU cc_start: 0.8925 (mp0) cc_final: 0.8380 (mm-30) REVERT: d 148 LEU cc_start: 0.8251 (mt) cc_final: 0.7974 (mt) REVERT: d 331 ASP cc_start: 0.6516 (p0) cc_final: 0.6125 (t70) REVERT: d 348 ILE cc_start: 0.9100 (mt) cc_final: 0.8753 (tt) REVERT: d 373 MET cc_start: 0.8877 (mmp) cc_final: 0.8622 (tpp) REVERT: d 457 MET cc_start: 0.9179 (mtt) cc_final: 0.8614 (mmm) REVERT: d 993 GLU cc_start: 0.7582 (tt0) cc_final: 0.7359 (tt0) REVERT: d 1182 ASP cc_start: 0.8451 (p0) cc_final: 0.7947 (p0) REVERT: d 1222 SER cc_start: 0.9329 (t) cc_final: 0.8726 (p) REVERT: d 1279 ARG cc_start: 0.7889 (mtm180) cc_final: 0.6770 (tpm170) REVERT: e 50 LYS cc_start: 0.8778 (pttt) cc_final: 0.8443 (ptpp) REVERT: e 69 ASN cc_start: 0.9044 (t0) cc_final: 0.8497 (t0) outliers start: 3 outliers final: 0 residues processed: 331 average time/residue: 0.1716 time to fit residues: 85.1960 Evaluate side-chains 227 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 210 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 180 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 260 optimal weight: 8.9990 chunk 256 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1042 HIS d 349 ASN d 368 ASN d 415 GLN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 687 GLN e 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.090145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066944 restraints weight = 94813.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068869 restraints weight = 54287.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070131 restraints weight = 37153.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070858 restraints weight = 28777.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071550 restraints weight = 24486.474| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22877 Z= 0.131 Angle : 0.591 11.124 30996 Z= 0.299 Chirality : 0.044 0.184 3523 Planarity : 0.004 0.053 4096 Dihedral : 4.080 19.480 3171 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2877 helix: 0.94 (0.16), residues: 1044 sheet: -0.75 (0.31), residues: 284 loop : -1.00 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 695 TYR 0.030 0.002 TYR c 731 PHE 0.022 0.002 PHE c 252 TRP 0.010 0.001 TRP d 105 HIS 0.005 0.001 HIS b 61 Details of bonding type rmsd covalent geometry : bond 0.00292 (22869) covalent geometry : angle 0.58075 (30984) hydrogen bonds : bond 0.04289 ( 897) hydrogen bonds : angle 4.94413 ( 2577) metal coordination : bond 0.01059 ( 8) metal coordination : angle 5.47315 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.770 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 103 MET cc_start: 0.4785 (tpt) cc_final: 0.4522 (tpt) REVERT: c 160 MET cc_start: 0.9008 (tpt) cc_final: 0.8775 (mmm) REVERT: c 393 MET cc_start: 0.8530 (ttm) cc_final: 0.8134 (ttp) REVERT: c 396 MET cc_start: 0.8338 (tmm) cc_final: 0.8110 (tmm) REVERT: c 513 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7316 (mm-30) REVERT: c 593 MET cc_start: 0.8581 (ppp) cc_final: 0.8311 (ppp) REVERT: c 724 MET cc_start: 0.8403 (ppp) cc_final: 0.7747 (ppp) REVERT: c 883 ASP cc_start: 0.7629 (m-30) cc_final: 0.7275 (m-30) REVERT: c 904 MET cc_start: 0.8992 (mmm) cc_final: 0.8569 (mmm) REVERT: c 1076 MET cc_start: 0.9010 (mmm) cc_final: 0.8343 (mmm) REVERT: c 1077 GLN cc_start: 0.9047 (mt0) cc_final: 0.8704 (mt0) REVERT: c 1119 GLU cc_start: 0.7206 (mp0) cc_final: 0.6888 (mp0) REVERT: d 142 GLU cc_start: 0.8898 (mp0) cc_final: 0.8395 (mm-30) REVERT: d 148 LEU cc_start: 0.8204 (mt) cc_final: 0.7896 (mt) REVERT: d 163 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7276 (pp20) REVERT: d 331 ASP cc_start: 0.6465 (p0) cc_final: 0.6169 (t70) REVERT: d 348 ILE cc_start: 0.9200 (mt) cc_final: 0.8883 (tt) REVERT: d 373 MET cc_start: 0.8819 (mmp) cc_final: 0.8570 (mmm) REVERT: d 457 MET cc_start: 0.9051 (mtt) cc_final: 0.8597 (mmm) REVERT: d 509 ILE cc_start: 0.9373 (mm) cc_final: 0.9155 (tp) REVERT: d 747 ASP cc_start: 0.8956 (t70) cc_final: 0.8631 (t70) REVERT: d 750 GLU cc_start: 0.8604 (pt0) cc_final: 0.8320 (pp20) REVERT: d 1010 LEU cc_start: 0.8032 (tp) cc_final: 0.7762 (tp) REVERT: d 1279 ARG cc_start: 0.7864 (mtm180) cc_final: 0.6764 (tpm170) REVERT: e 69 ASN cc_start: 0.9069 (t0) cc_final: 0.8748 (t0) REVERT: e 97 ARG cc_start: 0.9219 (ttp-110) cc_final: 0.8994 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1550 time to fit residues: 72.9165 Evaluate side-chains 225 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 262 optimal weight: 20.0000 chunk 241 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 277 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 505 HIS ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3740 r_free = 0.3740 target = 0.089362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066141 restraints weight = 95888.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068052 restraints weight = 54968.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069321 restraints weight = 37538.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070130 restraints weight = 29064.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070718 restraints weight = 24528.761| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22877 Z= 0.133 Angle : 0.579 10.317 30996 Z= 0.293 Chirality : 0.043 0.238 3523 Planarity : 0.004 0.056 4096 Dihedral : 3.985 18.085 3171 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2877 helix: 1.07 (0.16), residues: 1031 sheet: -0.75 (0.30), residues: 305 loop : -0.88 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 218 TYR 0.019 0.001 TYR d1142 PHE 0.016 0.001 PHE d 268 TRP 0.010 0.001 TRP d 484 HIS 0.004 0.001 HIS b 61 Details of bonding type rmsd covalent geometry : bond 0.00299 (22869) covalent geometry : angle 0.57157 (30984) hydrogen bonds : bond 0.04028 ( 897) hydrogen bonds : angle 4.74071 ( 2577) metal coordination : bond 0.00836 ( 8) metal coordination : angle 4.86753 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.650 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 393 MET cc_start: 0.8556 (ttm) cc_final: 0.8152 (ttp) REVERT: c 396 MET cc_start: 0.8443 (tmm) cc_final: 0.8191 (tmm) REVERT: c 593 MET cc_start: 0.8694 (ppp) cc_final: 0.7730 (ppp) REVERT: c 612 GLN cc_start: 0.8390 (tt0) cc_final: 0.7837 (tt0) REVERT: c 883 ASP cc_start: 0.7662 (m-30) cc_final: 0.7286 (m-30) REVERT: c 926 MET cc_start: 0.8885 (tpp) cc_final: 0.8560 (tpp) REVERT: c 1076 MET cc_start: 0.9195 (mmm) cc_final: 0.8529 (mmm) REVERT: c 1077 GLN cc_start: 0.9062 (mt0) cc_final: 0.8710 (mt0) REVERT: c 1094 ASP cc_start: 0.8506 (m-30) cc_final: 0.8197 (m-30) REVERT: c 1119 GLU cc_start: 0.7439 (mp0) cc_final: 0.6916 (mp0) REVERT: d 92 MET cc_start: 0.8389 (mmp) cc_final: 0.7872 (mmm) REVERT: d 142 GLU cc_start: 0.8877 (mp0) cc_final: 0.8308 (mm-30) REVERT: d 148 LEU cc_start: 0.8156 (mt) cc_final: 0.7814 (mt) REVERT: d 256 MET cc_start: 0.6378 (mtp) cc_final: 0.5125 (mtp) REVERT: d 348 ILE cc_start: 0.9233 (mt) cc_final: 0.8915 (tt) REVERT: d 373 MET cc_start: 0.8852 (mmp) cc_final: 0.8589 (mmm) REVERT: d 747 ASP cc_start: 0.8938 (t70) cc_final: 0.8614 (t70) REVERT: d 750 GLU cc_start: 0.8653 (pt0) cc_final: 0.8402 (pp20) REVERT: d 1010 LEU cc_start: 0.8049 (tp) cc_final: 0.7820 (tp) REVERT: d 1073 GLU cc_start: 0.6813 (pp20) cc_final: 0.6571 (pp20) REVERT: d 1222 SER cc_start: 0.9148 (m) cc_final: 0.8261 (p) REVERT: e 69 ASN cc_start: 0.9183 (t0) cc_final: 0.8554 (t0) REVERT: e 94 ILE cc_start: 0.9130 (tp) cc_final: 0.8626 (tp) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1554 time to fit residues: 69.4488 Evaluate side-chains 215 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 151 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 chunk 245 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 612 GLN c 679 ASN ** c1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 882 GLN ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.065829 restraints weight = 94667.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067640 restraints weight = 54223.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068923 restraints weight = 37067.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069694 restraints weight = 28690.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070292 restraints weight = 24288.638| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22877 Z= 0.123 Angle : 0.569 9.885 30996 Z= 0.287 Chirality : 0.043 0.245 3523 Planarity : 0.004 0.048 4096 Dihedral : 3.953 19.148 3171 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2877 helix: 1.17 (0.16), residues: 1033 sheet: -0.53 (0.30), residues: 292 loop : -0.82 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 159 TYR 0.059 0.001 TYR d 134 PHE 0.014 0.001 PHE d 268 TRP 0.018 0.001 TRP d 484 HIS 0.003 0.001 HIS e 100 Details of bonding type rmsd covalent geometry : bond 0.00276 (22869) covalent geometry : angle 0.56377 (30984) hydrogen bonds : bond 0.03859 ( 897) hydrogen bonds : angle 4.60367 ( 2577) metal coordination : bond 0.00752 ( 8) metal coordination : angle 3.91927 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.871 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 99 PHE cc_start: 0.8572 (p90) cc_final: 0.8365 (p90) REVERT: c 160 MET cc_start: 0.8814 (mmm) cc_final: 0.8421 (mmm) REVERT: c 393 MET cc_start: 0.8573 (ttm) cc_final: 0.8121 (ttp) REVERT: c 396 MET cc_start: 0.8408 (tmm) cc_final: 0.8174 (tmm) REVERT: c 513 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7399 (mm-30) REVERT: c 593 MET cc_start: 0.8044 (ppp) cc_final: 0.7424 (ppp) REVERT: c 612 GLN cc_start: 0.8058 (mt0) cc_final: 0.7752 (mt0) REVERT: c 724 MET cc_start: 0.8393 (ppp) cc_final: 0.7698 (ppp) REVERT: c 883 ASP cc_start: 0.7686 (m-30) cc_final: 0.7318 (m-30) REVERT: c 904 MET cc_start: 0.8998 (mmm) cc_final: 0.8668 (mtp) REVERT: c 926 MET cc_start: 0.8888 (tpp) cc_final: 0.8599 (tpp) REVERT: c 1076 MET cc_start: 0.9234 (mmm) cc_final: 0.8688 (mmm) REVERT: c 1077 GLN cc_start: 0.9068 (mt0) cc_final: 0.8689 (mt0) REVERT: c 1094 ASP cc_start: 0.8415 (m-30) cc_final: 0.7479 (p0) REVERT: c 1132 CYS cc_start: 0.8285 (t) cc_final: 0.7831 (m) REVERT: d 142 GLU cc_start: 0.8822 (mp0) cc_final: 0.8233 (mm-30) REVERT: d 148 LEU cc_start: 0.8100 (mt) cc_final: 0.7755 (mt) REVERT: d 256 MET cc_start: 0.6814 (mtp) cc_final: 0.6416 (mtp) REVERT: d 310 MET cc_start: 0.8682 (mpp) cc_final: 0.8227 (mmt) REVERT: d 327 MET cc_start: 0.7030 (mmp) cc_final: 0.6765 (mmp) REVERT: d 348 ILE cc_start: 0.9249 (mt) cc_final: 0.8918 (tt) REVERT: d 373 MET cc_start: 0.8886 (mmp) cc_final: 0.8606 (mmm) REVERT: d 457 MET cc_start: 0.9024 (mmm) cc_final: 0.8477 (mmt) REVERT: d 747 ASP cc_start: 0.8908 (t70) cc_final: 0.8607 (t70) REVERT: d 750 GLU cc_start: 0.8667 (pt0) cc_final: 0.8411 (pp20) REVERT: d 1222 SER cc_start: 0.9093 (m) cc_final: 0.8679 (p) REVERT: e 69 ASN cc_start: 0.9153 (t0) cc_final: 0.8573 (t0) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1493 time to fit residues: 65.4451 Evaluate side-chains 208 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 177 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 275 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 372 HIS ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 494 HIS d 552 GLN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 761 GLN d 882 GLN d1119 HIS ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062547 restraints weight = 96205.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064253 restraints weight = 55277.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065445 restraints weight = 38114.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066251 restraints weight = 29713.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066700 restraints weight = 25159.571| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22877 Z= 0.234 Angle : 0.692 14.340 30996 Z= 0.352 Chirality : 0.045 0.289 3523 Planarity : 0.005 0.049 4096 Dihedral : 4.452 21.405 3171 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2877 helix: 0.99 (0.16), residues: 1028 sheet: -0.79 (0.28), residues: 320 loop : -0.91 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 89 TYR 0.039 0.002 TYR d 134 PHE 0.015 0.002 PHE d 268 TRP 0.013 0.002 TRP d 484 HIS 0.010 0.001 HIS d 689 Details of bonding type rmsd covalent geometry : bond 0.00519 (22869) covalent geometry : angle 0.68503 (30984) hydrogen bonds : bond 0.04529 ( 897) hydrogen bonds : angle 4.91229 ( 2577) metal coordination : bond 0.01515 ( 8) metal coordination : angle 4.85523 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.864 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: symmetry clash revert: symmetry clash REVERT: c 393 MET cc_start: 0.8270 (ttm) cc_final: 0.7641 (tpt) REVERT: c 396 MET cc_start: 0.8446 (tmm) cc_final: 0.7889 (tmm) REVERT: c 513 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7217 (mm-30) REVERT: c 593 MET cc_start: 0.8137 (ppp) cc_final: 0.7565 (ppp) REVERT: c 612 GLN cc_start: 0.8279 (mt0) cc_final: 0.7871 (mt0) REVERT: c 724 MET cc_start: 0.8613 (ppp) cc_final: 0.7754 (ppp) REVERT: c 881 ASP cc_start: 0.8291 (t0) cc_final: 0.8078 (t0) REVERT: c 883 ASP cc_start: 0.7620 (m-30) cc_final: 0.7151 (m-30) REVERT: c 926 MET cc_start: 0.8978 (tpp) cc_final: 0.8727 (tpp) REVERT: c 1076 MET cc_start: 0.9277 (mmm) cc_final: 0.8908 (mmm) REVERT: d 138 SER cc_start: 0.8344 (p) cc_final: 0.8142 (p) REVERT: d 142 GLU cc_start: 0.8726 (mp0) cc_final: 0.8101 (mm-30) REVERT: d 148 LEU cc_start: 0.7856 (mt) cc_final: 0.7590 (mt) REVERT: d 256 MET cc_start: 0.6479 (mtp) cc_final: 0.5937 (mtp) REVERT: d 310 MET cc_start: 0.8818 (mpp) cc_final: 0.8352 (mmm) REVERT: d 327 MET cc_start: 0.7422 (mmp) cc_final: 0.7134 (mmp) REVERT: d 348 ILE cc_start: 0.9352 (mt) cc_final: 0.9014 (tt) REVERT: d 457 MET cc_start: 0.9106 (mmm) cc_final: 0.8565 (mmt) REVERT: d 576 MET cc_start: 0.8655 (ppp) cc_final: 0.8410 (ppp) REVERT: d 736 VAL cc_start: 0.8912 (t) cc_final: 0.8624 (t) REVERT: d 750 GLU cc_start: 0.8800 (pt0) cc_final: 0.8549 (pp20) REVERT: d 1222 SER cc_start: 0.9149 (m) cc_final: 0.8761 (p) REVERT: e 69 ASN cc_start: 0.9233 (t0) cc_final: 0.8618 (t0) REVERT: e 97 ARG cc_start: 0.9073 (ttp-110) cc_final: 0.8773 (ttp80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1563 time to fit residues: 61.8767 Evaluate side-chains 190 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 157 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 255 optimal weight: 0.0980 chunk 52 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 263 optimal weight: 0.0980 chunk 266 optimal weight: 0.7980 chunk 257 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3726 r_free = 0.3726 target = 0.088536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066002 restraints weight = 93566.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067848 restraints weight = 52253.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069099 restraints weight = 35287.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069965 restraints weight = 27094.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070430 restraints weight = 22740.154| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22877 Z= 0.108 Angle : 0.583 11.073 30996 Z= 0.294 Chirality : 0.043 0.175 3523 Planarity : 0.004 0.079 4096 Dihedral : 4.049 19.202 3171 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2877 helix: 1.14 (0.16), residues: 1031 sheet: -0.63 (0.28), residues: 327 loop : -0.75 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG d 556 TYR 0.023 0.001 TYR d 134 PHE 0.012 0.001 PHE d 268 TRP 0.025 0.001 TRP c 243 HIS 0.005 0.001 HIS c 200 Details of bonding type rmsd covalent geometry : bond 0.00231 (22869) covalent geometry : angle 0.57465 (30984) hydrogen bonds : bond 0.03769 ( 897) hydrogen bonds : angle 4.57307 ( 2577) metal coordination : bond 0.00800 ( 8) metal coordination : angle 5.12394 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.824 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 110 ILE cc_start: 0.8980 (mt) cc_final: 0.8747 (mt) REVERT: b 90 ASP cc_start: 0.8648 (p0) cc_final: 0.8413 (p0) REVERT: c 90 LEU cc_start: 0.8879 (pp) cc_final: 0.8510 (pp) REVERT: c 99 PHE cc_start: 0.8519 (p90) cc_final: 0.8282 (p90) REVERT: c 393 MET cc_start: 0.8224 (ttm) cc_final: 0.7660 (tpt) REVERT: c 396 MET cc_start: 0.8411 (tmm) cc_final: 0.7876 (tmm) REVERT: c 513 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7318 (mt-10) REVERT: c 593 MET cc_start: 0.8097 (ppp) cc_final: 0.7520 (ppp) REVERT: c 612 GLN cc_start: 0.8170 (mt0) cc_final: 0.7666 (mt0) REVERT: c 713 MET cc_start: 0.8037 (mmt) cc_final: 0.7737 (mmt) REVERT: c 883 ASP cc_start: 0.7559 (m-30) cc_final: 0.7209 (m-30) REVERT: c 926 MET cc_start: 0.8912 (tpp) cc_final: 0.8672 (tpp) REVERT: c 1051 MET cc_start: 0.9106 (mmp) cc_final: 0.8820 (mmm) REVERT: c 1076 MET cc_start: 0.9376 (mmm) cc_final: 0.8869 (mmm) REVERT: d 138 SER cc_start: 0.8254 (p) cc_final: 0.8028 (p) REVERT: d 142 GLU cc_start: 0.8753 (mp0) cc_final: 0.8435 (tp30) REVERT: d 148 LEU cc_start: 0.7884 (mt) cc_final: 0.7558 (mt) REVERT: d 256 MET cc_start: 0.6706 (mtp) cc_final: 0.6165 (mtp) REVERT: d 310 MET cc_start: 0.8622 (mpp) cc_final: 0.8064 (mmm) REVERT: d 348 ILE cc_start: 0.9301 (mt) cc_final: 0.8936 (tp) REVERT: d 373 MET cc_start: 0.9054 (mmp) cc_final: 0.8607 (mtp) REVERT: d 457 MET cc_start: 0.9083 (mmm) cc_final: 0.8567 (mmt) REVERT: d 750 GLU cc_start: 0.8706 (pt0) cc_final: 0.8484 (pp20) REVERT: d 1010 LEU cc_start: 0.8410 (tp) cc_final: 0.8186 (tp) REVERT: d 1222 SER cc_start: 0.9077 (m) cc_final: 0.8683 (p) REVERT: e 69 ASN cc_start: 0.9163 (t0) cc_final: 0.8654 (t0) REVERT: e 94 ILE cc_start: 0.9128 (tp) cc_final: 0.8868 (tp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1487 time to fit residues: 66.3543 Evaluate side-chains 202 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 241 optimal weight: 0.0030 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3715 r_free = 0.3715 target = 0.087982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065561 restraints weight = 93859.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067392 restraints weight = 52728.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068664 restraints weight = 35774.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069486 restraints weight = 27402.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069942 restraints weight = 23042.965| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22877 Z= 0.113 Angle : 0.582 10.067 30996 Z= 0.293 Chirality : 0.043 0.327 3523 Planarity : 0.004 0.079 4096 Dihedral : 3.952 18.453 3171 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2877 helix: 1.25 (0.16), residues: 1022 sheet: -0.48 (0.28), residues: 336 loop : -0.68 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 97 TYR 0.021 0.001 TYR d 134 PHE 0.010 0.001 PHE a 189 TRP 0.024 0.001 TRP d 105 HIS 0.004 0.001 HIS c 479 Details of bonding type rmsd covalent geometry : bond 0.00253 (22869) covalent geometry : angle 0.57601 (30984) hydrogen bonds : bond 0.03727 ( 897) hydrogen bonds : angle 4.51192 ( 2577) metal coordination : bond 0.00850 ( 8) metal coordination : angle 4.41095 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.832 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: symmetry clash revert: symmetry clash REVERT: b 90 ASP cc_start: 0.8756 (p0) cc_final: 0.8446 (p0) REVERT: c 99 PHE cc_start: 0.8510 (p90) cc_final: 0.8244 (p90) REVERT: c 154 MET cc_start: 0.8131 (mpp) cc_final: 0.7833 (mpp) REVERT: c 396 MET cc_start: 0.8574 (tmm) cc_final: 0.8243 (tmm) REVERT: c 513 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7482 (mm-30) REVERT: c 593 MET cc_start: 0.8012 (ppp) cc_final: 0.7416 (ppp) REVERT: c 612 GLN cc_start: 0.8148 (mt0) cc_final: 0.7624 (mt0) REVERT: c 661 MET cc_start: 0.7731 (mmp) cc_final: 0.7494 (mmm) REVERT: c 713 MET cc_start: 0.8084 (mmt) cc_final: 0.7836 (mmt) REVERT: c 724 MET cc_start: 0.8459 (ppp) cc_final: 0.7677 (ppp) REVERT: c 727 GLU cc_start: 0.8477 (mp0) cc_final: 0.8275 (mp0) REVERT: c 883 ASP cc_start: 0.7527 (m-30) cc_final: 0.7112 (m-30) REVERT: c 926 MET cc_start: 0.8907 (tpp) cc_final: 0.8679 (tpp) REVERT: c 988 LEU cc_start: 0.9091 (mm) cc_final: 0.8795 (tp) REVERT: c 1051 MET cc_start: 0.9142 (mmp) cc_final: 0.8836 (mmm) REVERT: c 1076 MET cc_start: 0.9352 (mmm) cc_final: 0.8975 (mmm) REVERT: d 138 SER cc_start: 0.8294 (p) cc_final: 0.8075 (p) REVERT: d 142 GLU cc_start: 0.8792 (mp0) cc_final: 0.8310 (mm-30) REVERT: d 143 MET cc_start: 0.9154 (tpt) cc_final: 0.8847 (tpt) REVERT: d 148 LEU cc_start: 0.7806 (mt) cc_final: 0.7483 (mt) REVERT: d 256 MET cc_start: 0.6857 (mtp) cc_final: 0.6376 (mtp) REVERT: d 310 MET cc_start: 0.8686 (mpp) cc_final: 0.8117 (mmm) REVERT: d 373 MET cc_start: 0.9063 (mmp) cc_final: 0.8619 (mtp) REVERT: d 457 MET cc_start: 0.9085 (mmm) cc_final: 0.8591 (mmt) REVERT: d 543 VAL cc_start: 0.9535 (t) cc_final: 0.9313 (m) REVERT: d 750 GLU cc_start: 0.8716 (pt0) cc_final: 0.8490 (pp20) REVERT: d 1222 SER cc_start: 0.9093 (m) cc_final: 0.8723 (p) REVERT: e 69 ASN cc_start: 0.9177 (t0) cc_final: 0.8714 (t0) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1488 time to fit residues: 64.4742 Evaluate side-chains 207 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 386 GLN ** c 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3647 r_free = 0.3647 target = 0.084522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062087 restraints weight = 95353.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063824 restraints weight = 54320.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064967 restraints weight = 37301.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065791 restraints weight = 29053.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066234 restraints weight = 24487.597| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22877 Z= 0.236 Angle : 0.706 14.996 30996 Z= 0.358 Chirality : 0.046 0.331 3523 Planarity : 0.005 0.050 4096 Dihedral : 4.482 19.743 3171 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2877 helix: 1.02 (0.16), residues: 1021 sheet: -0.77 (0.26), residues: 361 loop : -0.83 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 97 TYR 0.023 0.002 TYR d 793 PHE 0.018 0.002 PHE b 219 TRP 0.024 0.002 TRP c 243 HIS 0.007 0.001 HIS c 200 Details of bonding type rmsd covalent geometry : bond 0.00526 (22869) covalent geometry : angle 0.69737 (30984) hydrogen bonds : bond 0.04595 ( 897) hydrogen bonds : angle 4.87306 ( 2577) metal coordination : bond 0.01523 ( 8) metal coordination : angle 5.72838 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.900 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: symmetry clash revert: symmetry clash REVERT: b 90 ASP cc_start: 0.8844 (p0) cc_final: 0.8485 (p0) REVERT: b 191 LYS cc_start: 0.8935 (tttp) cc_final: 0.8676 (ttmm) REVERT: c 393 MET cc_start: 0.8392 (ttp) cc_final: 0.8116 (ttp) REVERT: c 396 MET cc_start: 0.8513 (tmm) cc_final: 0.8118 (tmm) REVERT: c 513 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7471 (mm-30) REVERT: c 593 MET cc_start: 0.8115 (ppp) cc_final: 0.6947 (ppp) REVERT: c 612 GLN cc_start: 0.8362 (mt0) cc_final: 0.8051 (mt0) REVERT: c 724 MET cc_start: 0.8570 (ppp) cc_final: 0.7738 (ppp) REVERT: c 883 ASP cc_start: 0.7572 (m-30) cc_final: 0.7089 (m-30) REVERT: c 926 MET cc_start: 0.9005 (tpp) cc_final: 0.8783 (tpp) REVERT: c 1051 MET cc_start: 0.9150 (mmp) cc_final: 0.8827 (mmm) REVERT: c 1111 ASN cc_start: 0.8655 (p0) cc_final: 0.8450 (p0) REVERT: d 142 GLU cc_start: 0.8833 (mp0) cc_final: 0.8300 (mm-30) REVERT: d 143 MET cc_start: 0.9147 (tpt) cc_final: 0.8826 (tpt) REVERT: d 148 LEU cc_start: 0.7672 (mt) cc_final: 0.7320 (mt) REVERT: d 256 MET cc_start: 0.6662 (mtp) cc_final: 0.6203 (mtp) REVERT: d 310 MET cc_start: 0.8771 (mpp) cc_final: 0.8142 (mmt) REVERT: d 457 MET cc_start: 0.9080 (mmm) cc_final: 0.8565 (mmt) REVERT: d 1222 SER cc_start: 0.9252 (m) cc_final: 0.8883 (p) REVERT: e 69 ASN cc_start: 0.9267 (t0) cc_final: 0.8674 (t0) REVERT: e 97 ARG cc_start: 0.9141 (ttp-110) cc_final: 0.8936 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1511 time to fit residues: 59.6688 Evaluate side-chains 189 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 266 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 177 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1054 GLN ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3701 r_free = 0.3701 target = 0.087205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064779 restraints weight = 94509.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066590 restraints weight = 53111.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067861 restraints weight = 35917.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068696 restraints weight = 27543.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069199 restraints weight = 23093.193| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22877 Z= 0.116 Angle : 0.621 12.198 30996 Z= 0.313 Chirality : 0.044 0.290 3523 Planarity : 0.005 0.106 4096 Dihedral : 4.143 19.441 3171 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.04 % Allowed : 0.12 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2877 helix: 1.11 (0.16), residues: 1026 sheet: -0.51 (0.28), residues: 340 loop : -0.69 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 282 TYR 0.021 0.001 TYR d 793 PHE 0.015 0.001 PHE a 63 TRP 0.029 0.002 TRP d 105 HIS 0.015 0.001 HIS d 103 Details of bonding type rmsd covalent geometry : bond 0.00255 (22869) covalent geometry : angle 0.61463 (30984) hydrogen bonds : bond 0.03861 ( 897) hydrogen bonds : angle 4.62816 ( 2577) metal coordination : bond 0.00697 ( 8) metal coordination : angle 4.39282 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.789 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 ASP cc_start: 0.8733 (p0) cc_final: 0.8399 (p0) REVERT: c 136 THR cc_start: 0.8552 (p) cc_final: 0.8332 (t) REVERT: c 393 MET cc_start: 0.8446 (ttp) cc_final: 0.7801 (tpp) REVERT: c 396 MET cc_start: 0.8446 (tmm) cc_final: 0.7660 (tmm) REVERT: c 513 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7345 (mm-30) REVERT: c 593 MET cc_start: 0.8078 (ppp) cc_final: 0.6885 (ppp) REVERT: c 612 GLN cc_start: 0.8161 (mt0) cc_final: 0.7926 (mt0) REVERT: c 727 GLU cc_start: 0.8527 (mp0) cc_final: 0.8295 (mp0) REVERT: c 883 ASP cc_start: 0.7337 (m-30) cc_final: 0.6921 (m-30) REVERT: c 926 MET cc_start: 0.8900 (tpp) cc_final: 0.8674 (tpp) REVERT: c 988 LEU cc_start: 0.9103 (mm) cc_final: 0.8901 (tp) REVERT: c 1051 MET cc_start: 0.9128 (mmp) cc_final: 0.8849 (mmm) REVERT: c 1076 MET cc_start: 0.9033 (tpt) cc_final: 0.8786 (tpp) REVERT: c 1077 GLN cc_start: 0.8930 (mt0) cc_final: 0.8593 (mt0) REVERT: c 1111 ASN cc_start: 0.8557 (p0) cc_final: 0.8334 (p0) REVERT: d 89 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7753 (mmm-85) REVERT: d 138 SER cc_start: 0.8292 (p) cc_final: 0.8080 (p) REVERT: d 142 GLU cc_start: 0.8806 (mp0) cc_final: 0.8444 (mm-30) REVERT: d 143 MET cc_start: 0.9110 (tpt) cc_final: 0.8798 (tpt) REVERT: d 148 LEU cc_start: 0.7758 (mt) cc_final: 0.7443 (mt) REVERT: d 256 MET cc_start: 0.6731 (mtp) cc_final: 0.6308 (mtp) REVERT: d 310 MET cc_start: 0.8691 (mpp) cc_final: 0.8144 (mmm) REVERT: d 373 MET cc_start: 0.9432 (mmm) cc_final: 0.8890 (mtp) REVERT: d 457 MET cc_start: 0.9084 (mmm) cc_final: 0.8622 (mmt) REVERT: d 950 ASP cc_start: 0.9240 (m-30) cc_final: 0.9031 (m-30) REVERT: d 1222 SER cc_start: 0.9187 (m) cc_final: 0.8817 (p) REVERT: e 69 ASN cc_start: 0.9113 (t0) cc_final: 0.8688 (t0) REVERT: e 97 ARG cc_start: 0.9057 (ttp-110) cc_final: 0.8842 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1505 time to fit residues: 61.8753 Evaluate side-chains 194 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 272 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 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 = 0.3664 r_free = 0.3664 target = 0.085307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062747 restraints weight = 95757.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064431 restraints weight = 54786.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065635 restraints weight = 37739.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066333 restraints weight = 29272.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066928 restraints weight = 24943.179| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22877 Z= 0.181 Angle : 0.653 13.673 30996 Z= 0.330 Chirality : 0.045 0.271 3523 Planarity : 0.005 0.093 4096 Dihedral : 4.288 18.935 3171 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2877 helix: 1.06 (0.16), residues: 1027 sheet: -0.68 (0.27), residues: 342 loop : -0.71 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 97 TYR 0.027 0.002 TYR d 793 PHE 0.019 0.002 PHE d 673 TRP 0.030 0.002 TRP d 105 HIS 0.006 0.001 HIS c 200 Details of bonding type rmsd covalent geometry : bond 0.00405 (22869) covalent geometry : angle 0.64561 (30984) hydrogen bonds : bond 0.04168 ( 897) hydrogen bonds : angle 4.73462 ( 2577) metal coordination : bond 0.01252 ( 8) metal coordination : angle 4.87613 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.32 seconds wall clock time: 70 minutes 17.07 seconds (4217.07 seconds total)