Starting phenix.real_space_refine (version: dev) on Fri Feb 24 21:17:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp4_13579/02_2023/7pp4_13579.pdb" } resolution = 3.84 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 ------------------------------------------------------------------------------- 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= -0.004 sd= 0.046 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 Process input model Symmetric amino acids flipped Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23816 Number of models: 1 Model: "" Number of chains: 7 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: 8640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8640 Classifications: {'peptide': 1112} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1049} Chain: "d" Number of atoms: 9951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9951 Classifications: {'peptide': 1269} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Chain: "e" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 654 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "f" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1119 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} 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 19145 SG CYS d 891 53.286 82.541 99.359 1.00 41.50 S ATOM 19719 SG CYS d 968 56.209 82.943 96.563 1.00 46.68 S ATOM 19761 SG CYS d 975 54.610 79.648 97.691 1.00 39.55 S ATOM 19779 SG CYS d 978 52.612 81.879 95.678 1.00 42.32 S ATOM 12565 SG CYS d 60 121.649 72.008 93.859 1.00112.36 S ATOM 12583 SG CYS d 62 124.257 73.067 94.827 1.00113.61 S ATOM 12692 SG CYS d 75 122.413 73.710 97.707 1.00114.67 S ATOM 12718 SG CYS d 78 121.212 75.331 95.336 1.00112.81 S Time building chain proxies: 13.04, per 1000 atoms: 0.55 Number of scatterers: 23816 At special positions: 0 Unit cell: (151.8, 185.9, 129.8, 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 87 16.00 Mg 1 11.99 O 4565 8.00 N 4233 7.00 C 14928 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 - 3.50 Amino acid : False - 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: 10.25 Conformation dependent library (CDL) restraints added in 3.7 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 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " Number of angles added : 12 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 44 sheets defined 41.3% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 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: 4.315A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 5.090A 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: 3.983A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.189A 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: 3.948A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.827A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 4.115A 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: 3.660A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.940A 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: 3.680A 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: 3.564A 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: 3.595A pdb=" N MET c 593 " --> pdb=" O ALA c 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 590 through 594' Processing helix chain 'c' and resid 601 through 613 removed outlier: 3.775A 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 730 through 732 No H-bonds generated for 'chain 'c' and resid 730 through 732' Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 814 through 825 removed outlier: 3.900A pdb=" N ARG c 819 " --> pdb=" O THR c 815 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU c 820 " --> pdb=" O PRO c 816 " (cutoff:3.500A) Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.172A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 removed outlier: 3.553A 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: 3.611A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 removed outlier: 3.563A 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: 4.214A pdb=" N ARG d 91 " --> pdb=" O ARG d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.792A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) removed outlier: 3.542A 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 130 Processing helix chain 'd' and resid 140 through 147 removed outlier: 3.515A pdb=" N GLU d 147 " --> pdb=" O MET d 143 " (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 257 through 268 removed outlier: 3.516A pdb=" N ILE d 261 " --> pdb=" O GLY d 257 " (cutoff:3.500A) Processing helix chain 'd' and resid 270 through 283 Processing helix chain 'd' and resid 285 through 306 removed outlier: 4.148A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix 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: 3.609A 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 removed outlier: 3.523A pdb=" N ASN d 416 " --> pdb=" O ARG d 412 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 452 removed outlier: 3.912A 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: 3.700A 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 removed outlier: 3.532A pdb=" N PHE d 532 " --> pdb=" O VAL d 528 " (cutoff:3.500A) Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 removed outlier: 3.592A pdb=" N ASN d 563 " --> pdb=" O LEU d 560 " (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: 4.074A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE d 651 " --> pdb=" O GLU d 647 " (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 726 removed outlier: 4.023A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG d 726 " --> pdb=" O TYR d 722 " (cutoff:3.500A) Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.672A 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: 3.743A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.551A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA d 868 " --> pdb=" O ALA d 864 " (cutoff:3.500A) removed outlier: 3.779A 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 Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.885A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.055A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.853A 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: 3.668A 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: 3.692A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 4.485A pdb=" N TYR d1283 " --> pdb=" O ARG d1279 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 47 removed outlier: 3.996A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG e 46 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 70 removed outlier: 3.560A pdb=" N VAL e 54 " --> pdb=" O LYS e 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 73 No H-bonds generated for 'chain 'e' and resid 71 through 73' Processing helix chain 'e' and resid 90 through 100 Processing helix chain 'f' and resid 25 through 35 Processing helix chain 'f' and resid 44 through 65 Processing helix chain 'f' and resid 73 through 94 removed outlier: 3.621A pdb=" N ASN f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 105 removed outlier: 3.692A pdb=" N TYR f 105 " --> pdb=" O LEU f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 128 removed outlier: 3.745A pdb=" N GLU f 128 " --> pdb=" O ILE f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.987A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 13 removed outlier: 3.688A 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: 6.436A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 3.543A 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: 5.578A 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: 3.576A pdb=" N SER a 86 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.555A 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: 6.714A 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: 6.714A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.874A 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: 6.204A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE b 54 " --> pdb=" O ILE b 162 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.891A 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: 4.130A 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: 4.777A pdb=" N LEU c 105 " --> pdb=" O ILE c 140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE c 140 " --> pdb=" O LEU c 105 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE c 107 " --> pdb=" O GLU c 138 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU c 138 " --> pdb=" O PHE c 107 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP c 109 " --> pdb=" O THR c 136 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR c 136 " --> pdb=" O ASP c 109 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.746A 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 Processing sheet with id=AB4, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.588A pdb=" N GLN c 178 " --> pdb=" O ARG c 379 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER c 177 " --> pdb=" O SER c 456 " (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: 3.600A 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 558 through 559 removed outlier: 3.602A pdb=" N VAL c 559 " --> pdb=" O VAL c 571 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL c 571 " --> pdb=" O VAL c 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'c' and resid 667 through 671 removed outlier: 6.952A 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: 7.634A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 676 through 677 removed outlier: 3.548A pdb=" N ALA c 676 " --> pdb=" O ALA c 684 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA c 684 " --> pdb=" O ALA c 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'c' and resid 687 through 688 removed outlier: 3.523A pdb=" N ASP c 704 " --> pdb=" O CYS c 687 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.170A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU c 719 " --> pdb=" O MET c1028 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE c 735 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE c 898 " --> pdb=" O ILE c 735 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU c 737 " --> pdb=" O ILE c 898 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.170A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 748 through 752 removed outlier: 6.710A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 748 through 752 removed outlier: 4.028A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.888A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 806 through 808 Processing sheet with id=AD1, first strand: chain 'c' and resid 906 through 907 removed outlier: 3.577A pdb=" N PHE c 906 " --> pdb=" O PHE c1011 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.789A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET d 541 " --> pdb=" O SER d 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 7.737A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 1133 through 1135 Processing sheet with id=AD5, first strand: chain 'd' and resid 9 through 10 Processing sheet with id=AD6, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AD7, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD8, first strand: chain 'd' and resid 134 through 135 removed outlier: 3.767A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.833A pdb=" N SER d 138 " --> pdb=" O THR d 253 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.384A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.536A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU d 637 " --> pdb=" O TRP d 662 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.536A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.742A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 902 through 903 Processing sheet with id=AE6, first strand: chain 'd' and resid 1075 through 1080 removed outlier: 4.244A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY d1051 " --> pdb=" O VAL d1105 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL d1105 " --> pdb=" O GLY d1051 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 1181 through 1182 removed outlier: 3.751A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 1272 through 1274 1008 hydrogen bonds defined for protein. 2847 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: 9.30 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8171 1.34 - 1.46: 2681 1.46 - 1.57: 13214 1.57 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 24219 Sorted by residual: bond pdb=" N VAL d 974 " pdb=" CA VAL d 974 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.76e+00 bond pdb=" N ASP d 539 " pdb=" CA ASP d 539 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.54e+00 bond pdb=" N THR d 970 " pdb=" CA THR d 970 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N ARG f 67 " pdb=" CA ARG f 67 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.64e+00 bond pdb=" N CYS d 891 " pdb=" CA CYS d 891 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.33e-02 5.65e+03 5.64e+00 ... (remaining 24214 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.55: 761 106.55 - 113.42: 13372 113.42 - 120.30: 8673 120.30 - 127.18: 9743 127.18 - 134.06: 250 Bond angle restraints: 32799 Sorted by residual: angle pdb=" CA ASP d 539 " pdb=" C ASP d 539 " pdb=" O ASP d 539 " ideal model delta sigma weight residual 121.56 116.63 4.93 1.09e+00 8.42e-01 2.04e+01 angle pdb=" C ASP d 535 " pdb=" CA ASP d 535 " pdb=" CB ASP d 535 " ideal model delta sigma weight residual 109.37 117.67 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N ASP d 535 " pdb=" CA ASP d 535 " pdb=" C ASP d 535 " ideal model delta sigma weight residual 109.40 103.06 6.34 1.63e+00 3.76e-01 1.51e+01 angle pdb=" CA ASP d 535 " pdb=" CB ASP d 535 " pdb=" CG ASP d 535 " ideal model delta sigma weight residual 112.60 116.45 -3.85 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA ARG f 67 " pdb=" C ARG f 67 " pdb=" O ARG f 67 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.42e+01 ... (remaining 32794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 14235 17.79 - 35.58: 539 35.58 - 53.37: 60 53.37 - 71.16: 14 71.16 - 88.95: 4 Dihedral angle restraints: 14852 sinusoidal: 6103 harmonic: 8749 Sorted by residual: 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 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+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 -164.59 -15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" N ARG d 478 " pdb=" CA ARG d 478 " pdb=" CB ARG d 478 " pdb=" CG ARG d 478 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 14849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2439 0.029 - 0.057: 792 0.057 - 0.086: 218 0.086 - 0.115: 219 0.115 - 0.144: 55 Chirality restraints: 3723 Sorted by residual: chirality pdb=" CA VAL c 561 " pdb=" N VAL c 561 " pdb=" C VAL c 561 " pdb=" CB VAL c 561 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE d 832 " pdb=" N ILE d 832 " pdb=" C ILE d 832 " pdb=" CB ILE d 832 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE c1117 " pdb=" N ILE c1117 " pdb=" C ILE c1117 " pdb=" CB ILE c1117 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 3720 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL c 571 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO c 572 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO c 572 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO c 572 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG b 6 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO b 7 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO b 7 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 7 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU c1125 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU c1125 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU c1125 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS c1126 " -0.009 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 172 2.52 - 3.12: 19429 3.12 - 3.71: 35072 3.71 - 4.31: 47040 4.31 - 4.90: 79982 Nonbonded interactions: 181695 Sorted by model distance: nonbonded pdb=" O PRO d 326 " pdb=" OG1 THR d 337 " model vdw 1.926 2.440 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.036 2.440 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 2.064 2.440 nonbonded pdb=" OH TYR d 241 " pdb=" O GLY d 254 " model vdw 2.067 2.440 nonbonded pdb=" O ARG d1054 " pdb=" OG1 THR d1065 " model vdw 2.119 2.440 ... (remaining 181690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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 87 5.16 5 C 14928 2.51 5 N 4233 2.21 5 O 4565 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.810 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: 20.690 Check model and map are aligned: 0.360 Process input model: 64.480 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.002 0.038 24219 Z= 0.160 Angle : 0.476 8.296 32799 Z= 0.264 Chirality : 0.040 0.144 3723 Planarity : 0.003 0.045 4332 Dihedral : 9.428 88.947 9232 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 3045 helix: 1.70 (0.16), residues: 1119 sheet: -1.46 (0.29), residues: 348 loop : -0.95 (0.16), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 478 time to evaluate : 2.824 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: symmetry clash outliers start: 10 outliers final: 3 residues processed: 485 average time/residue: 0.4485 time to fit residues: 316.5844 Evaluate side-chains 262 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2403 time to fit residues: 5.9013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 chunk 177 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 d 145 HIS d 207 GLN d1125 GLN ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN f 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24219 Z= 0.208 Angle : 0.604 10.435 32799 Z= 0.305 Chirality : 0.043 0.232 3723 Planarity : 0.004 0.054 4332 Dihedral : 3.634 17.003 3363 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 3045 helix: 1.55 (0.16), residues: 1143 sheet: -1.22 (0.27), residues: 359 loop : -0.87 (0.16), residues: 1543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 3.041 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 outliers start: 41 outliers final: 15 residues processed: 321 average time/residue: 0.3828 time to fit residues: 193.6047 Evaluate side-chains 253 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2289 time to fit residues: 10.2735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 0.0970 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 329 GLN d 761 GLN e 88 GLN f 20 GLN f 89 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 24219 Z= 0.330 Angle : 0.621 8.984 32799 Z= 0.318 Chirality : 0.043 0.168 3723 Planarity : 0.004 0.051 4332 Dihedral : 4.062 19.331 3363 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 3045 helix: 1.23 (0.16), residues: 1140 sheet: -1.31 (0.26), residues: 381 loop : -1.03 (0.16), residues: 1524 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 245 time to evaluate : 3.105 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 outliers start: 63 outliers final: 19 residues processed: 290 average time/residue: 0.3765 time to fit residues: 173.6711 Evaluate side-chains 234 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2083 time to fit residues: 11.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24219 Z= 0.215 Angle : 0.567 10.554 32799 Z= 0.286 Chirality : 0.043 0.330 3723 Planarity : 0.004 0.049 4332 Dihedral : 3.976 18.215 3363 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 3045 helix: 1.31 (0.16), residues: 1137 sheet: -1.24 (0.26), residues: 378 loop : -0.98 (0.16), residues: 1530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 2.841 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 outliers start: 47 outliers final: 19 residues processed: 276 average time/residue: 0.3722 time to fit residues: 163.8526 Evaluate side-chains 234 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 2.850 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2255 time to fit residues: 12.0189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 4.9990 chunk 166 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 250 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 693 GLN d 761 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 24219 Z= 0.308 Angle : 0.602 8.583 32799 Z= 0.307 Chirality : 0.043 0.445 3723 Planarity : 0.004 0.049 4332 Dihedral : 4.200 19.342 3363 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3045 helix: 1.19 (0.16), residues: 1140 sheet: -1.17 (0.27), residues: 369 loop : -1.06 (0.16), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 2.912 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 outliers start: 38 outliers final: 16 residues processed: 255 average time/residue: 0.3762 time to fit residues: 153.4365 Evaluate side-chains 222 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2155 time to fit residues: 10.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 298 ASN ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 24219 Z= 0.270 Angle : 0.598 8.947 32799 Z= 0.301 Chirality : 0.042 0.200 3723 Planarity : 0.004 0.051 4332 Dihedral : 4.184 19.894 3363 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3045 helix: 1.23 (0.16), residues: 1135 sheet: -1.12 (0.26), residues: 367 loop : -1.05 (0.16), residues: 1543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 2.965 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 outliers start: 32 outliers final: 19 residues processed: 242 average time/residue: 0.3788 time to fit residues: 145.9532 Evaluate side-chains 229 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 2.899 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2263 time to fit residues: 12.3218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24219 Z= 0.185 Angle : 0.566 9.930 32799 Z= 0.284 Chirality : 0.042 0.255 3723 Planarity : 0.004 0.051 4332 Dihedral : 4.042 21.698 3363 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 3045 helix: 1.32 (0.16), residues: 1133 sheet: -0.95 (0.27), residues: 363 loop : -1.00 (0.16), residues: 1549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 252 average time/residue: 0.4037 time to fit residues: 163.0799 Evaluate side-chains 223 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 2.925 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2376 time to fit residues: 7.2409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 0.0020 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 230 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 24219 Z= 0.176 Angle : 0.576 11.413 32799 Z= 0.287 Chirality : 0.042 0.195 3723 Planarity : 0.004 0.051 4332 Dihedral : 3.968 21.124 3363 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 3045 helix: 1.33 (0.16), residues: 1133 sheet: -0.82 (0.27), residues: 359 loop : -0.98 (0.16), residues: 1553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 2.900 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 outliers start: 13 outliers final: 5 residues processed: 247 average time/residue: 0.3798 time to fit residues: 150.6643 Evaluate side-chains 219 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 214 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2142 time to fit residues: 5.9615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.7980 chunk 280 optimal weight: 0.0670 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24219 Z= 0.192 Angle : 0.586 10.719 32799 Z= 0.292 Chirality : 0.042 0.196 3723 Planarity : 0.004 0.051 4332 Dihedral : 3.936 20.532 3363 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 3045 helix: 1.33 (0.16), residues: 1133 sheet: -0.86 (0.27), residues: 365 loop : -0.94 (0.16), residues: 1547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 3.477 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 outliers start: 13 outliers final: 7 residues processed: 230 average time/residue: 0.4064 time to fit residues: 151.1864 Evaluate side-chains 220 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 213 time to evaluate : 2.924 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2877 time to fit residues: 7.5664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 302 optimal weight: 0.0670 chunk 278 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24219 Z= 0.232 Angle : 0.600 10.614 32799 Z= 0.300 Chirality : 0.042 0.188 3723 Planarity : 0.004 0.051 4332 Dihedral : 3.988 20.457 3363 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 3045 helix: 1.32 (0.16), residues: 1133 sheet: -0.86 (0.27), residues: 366 loop : -0.97 (0.16), residues: 1546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 0.3802 time to fit residues: 134.5487 Evaluate side-chains 211 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 2.867 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2742 time to fit residues: 4.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068618 restraints weight = 66822.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070654 restraints weight = 38961.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072023 restraints weight = 27438.324| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 24219 Z= 0.344 Angle : 0.663 11.189 32799 Z= 0.336 Chirality : 0.044 0.223 3723 Planarity : 0.004 0.050 4332 Dihedral : 4.289 19.919 3363 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 3045 helix: 1.12 (0.16), residues: 1133 sheet: -1.06 (0.27), residues: 373 loop : -1.03 (0.16), residues: 1539 =============================================================================== Job complete usr+sys time: 4439.43 seconds wall clock time: 82 minutes 35.25 seconds (4955.25 seconds total)