Starting phenix.real_space_refine on Sat May 24 10:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjs_50511/05_2025/9fjs_50511.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15884 2.51 5 N 4527 2.21 5 O 4896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25413 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "b" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1759 Classifications: {'peptide': 231} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8742 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1063} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "f" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "O" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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 19281 SG CYS d 891 109.639 65.943 85.057 1.00 36.05 S ATOM 19855 SG CYS d 968 106.129 65.213 86.454 1.00 35.82 S ATOM 19897 SG CYS d 975 106.638 67.206 83.180 1.00 29.13 S ATOM 19915 SG CYS d 978 107.306 63.599 83.185 1.00 31.31 S ATOM 12701 SG CYS d 60 69.609 107.202 117.948 1.00 76.12 S ATOM 12719 SG CYS d 62 66.723 109.116 119.507 1.00 85.46 S ATOM 12828 SG CYS d 75 70.374 109.210 120.930 1.00 83.03 S ATOM 12854 SG CYS d 78 68.061 106.169 121.325 1.00 77.95 S Time building chain proxies: 14.69, per 1000 atoms: 0.58 Number of scatterers: 25413 At special positions: 0 Unit cell: (131.024, 144.816, 199.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 10 15.00 Mg 1 11.99 O 4896 8.00 N 4527 7.00 C 15884 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: 6.58 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " Number of angles added : 12 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 43 sheets defined 43.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.984A 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 225 removed outlier: 4.137A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 46 removed outlier: 4.010A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE b 46 " --> pdb=" O LEU b 42 " (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 203 through 225 removed outlier: 3.813A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 65 removed outlier: 4.096A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 removed outlier: 3.638A pdb=" N GLU c 76 " --> pdb=" O GLU c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 93 removed outlier: 3.826A pdb=" N TYR c 91 " --> pdb=" O GLU c 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 Processing helix chain 'c' and resid 226 through 229 Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 255 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 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 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 469 through 474 removed outlier: 3.893A pdb=" N ARG c 473 " --> pdb=" O GLY c 469 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP c 474 " --> pdb=" O LEU c 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 469 through 474' Processing helix chain 'c' and resid 532 through 539 removed outlier: 4.054A pdb=" N ARG c 538 " --> pdb=" O ASP c 534 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS c 539 " --> pdb=" O GLU c 535 " (cutoff:3.500A) Processing helix chain 'c' and resid 582 through 587 removed outlier: 4.459A pdb=" N MET c 586 " --> pdb=" O PRO c 583 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL c 587 " --> pdb=" O ARG c 584 " (cutoff:3.500A) Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.730A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 596 through 600 Processing helix chain 'c' and resid 601 through 612 Processing helix chain 'c' and resid 629 through 638 removed outlier: 4.382A pdb=" N ARG c 633 " --> pdb=" O GLY c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 815 through 826 Processing helix chain 'c' and resid 856 through 858 No H-bonds generated for 'chain 'c' and resid 856 through 858' Processing helix chain 'c' and resid 900 through 904 Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.263A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG c 925 " --> pdb=" O GLY c 921 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 960 through 964 removed outlier: 3.916A pdb=" N LEU c 964 " --> pdb=" O ASP c 961 " (cutoff:3.500A) Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.554A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 Processing helix chain 'c' and resid 1081 through 1090 removed outlier: 3.727A pdb=" N LEU c1085 " --> pdb=" O ALA c1081 " (cutoff:3.500A) 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 90 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 Processing helix chain 'd' and resid 147 through 187 Processing helix chain 'd' and resid 191 through 229 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'd' and resid 257 through 268 Processing helix chain 'd' and resid 270 through 283 removed outlier: 3.528A pdb=" N ASN d 283 " --> pdb=" O ASP d 279 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 304 Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.550A 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 321 through 325 Processing helix chain 'd' and resid 338 through 361 removed outlier: 4.033A pdb=" N ASP d 342 " --> pdb=" O SER d 338 " (cutoff:3.500A) Processing helix chain 'd' and resid 363 through 383 Processing helix chain 'd' and resid 401 through 406 removed outlier: 3.502A pdb=" N LEU d 405 " --> pdb=" O LEU d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 411 through 419 Processing helix chain 'd' and resid 445 through 452 removed outlier: 3.637A pdb=" N LEU d 449 " --> pdb=" O LYS d 445 " (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 481 through 491 removed outlier: 4.301A pdb=" N ASP d 485 " --> pdb=" O PRO d 481 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL d 486 " --> pdb=" O GLN d 482 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU d 489 " --> pdb=" O ASP d 485 " (cutoff:3.500A) removed outlier: 3.643A 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 528 through 533 Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 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: 3.787A 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 702 Processing helix chain 'd' and resid 705 through 726 removed outlier: 3.666A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG d 726 " --> pdb=" O TYR d 722 " (cutoff:3.500A) Processing helix chain 'd' and resid 742 through 762 Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 removed outlier: 3.882A pdb=" N VAL d 803 " --> pdb=" O ILE d 799 " (cutoff:3.500A) Processing helix chain 'd' and resid 810 through 817 removed outlier: 3.602A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.013A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA d 864 " --> pdb=" O LEU d 860 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU d 865 " --> pdb=" O ALA d 861 " (cutoff:3.500A) Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 964 through 968 Processing helix chain 'd' and resid 976 through 980 Processing helix chain 'd' and resid 994 through 1005 removed outlier: 3.699A pdb=" N VAL d 998 " --> pdb=" O ALA d 994 " (cutoff:3.500A) Processing helix chain 'd' and resid 1006 through 1009 Processing helix chain 'd' and resid 1027 through 1037 removed outlier: 3.535A pdb=" N VAL d1031 " --> pdb=" O GLY d1027 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1125 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.520A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1163 removed outlier: 4.499A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1182 through 1197 removed outlier: 4.041A pdb=" N ALA d1188 " --> pdb=" O ALA d1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d1189 " --> pdb=" O GLU d1185 " (cutoff:3.500A) Processing helix chain 'd' and resid 1211 through 1218 removed outlier: 3.647A pdb=" N THR d1217 " --> pdb=" O ALA d1213 " (cutoff:3.500A) Processing helix chain 'd' and resid 1219 through 1225 removed outlier: 4.141A pdb=" N SER d1225 " --> pdb=" O LEU d1221 " (cutoff:3.500A) Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1247 through 1255 removed outlier: 3.612A pdb=" N ILE d1253 " --> pdb=" O LYS d1249 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE d1254 " --> pdb=" O GLU d1250 " (cutoff:3.500A) Processing helix chain 'd' and resid 1264 through 1269 removed outlier: 3.866A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 3.628A pdb=" N TYR d1283 " --> pdb=" O ARG d1279 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 45 removed outlier: 3.791A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 71 removed outlier: 3.970A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 101 Processing helix chain 'f' and resid 25 through 37 removed outlier: 4.187A pdb=" N THR f 37 " --> pdb=" O GLY f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 63 removed outlier: 4.140A pdb=" N GLU f 63 " --> pdb=" O GLU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 103 removed outlier: 3.540A pdb=" N ARG f 74 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU f 97 " --> pdb=" O ALA f 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL f 98 " --> pdb=" O ASN f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 106 No H-bonds generated for 'chain 'f' and resid 104 through 106' Processing helix chain 'f' and resid 111 through 129 removed outlier: 3.562A pdb=" N LYS f 129 " --> pdb=" O ARG f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.791A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP f 144 " --> pdb=" O THR f 140 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP f 145 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 186 Processing helix chain 'f' and resid 190 through 199 Processing helix chain 'f' and resid 201 through 213 Processing helix chain 'f' and resid 229 through 234 removed outlier: 4.111A pdb=" N PHE f 233 " --> pdb=" O PRO f 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE f 234 " --> pdb=" O LEU f 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 229 through 234' Processing helix chain 'f' and resid 240 through 262 Processing helix chain 'f' and resid 263 through 275 Processing helix chain 'f' and resid 283 through 292 Processing helix chain 'f' and resid 296 through 310 removed outlier: 4.171A pdb=" N GLN f 300 " --> pdb=" O GLU f 296 " (cutoff:3.500A) Processing helix chain 'f' and resid 312 through 319 removed outlier: 3.633A pdb=" N ASP f 316 " --> pdb=" O GLY f 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 15 removed outlier: 3.633A pdb=" N GLU a 24 " --> pdb=" O THR a 8 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG a 18 " --> pdb=" O LEU a 14 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS a 191 " --> pdb=" O VAL a 178 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL a 178 " --> pdb=" O LYS a 191 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE a 193 " --> pdb=" O TYR a 176 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR a 176 " --> pdb=" O ILE a 193 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP a 195 " --> pdb=" O VAL a 174 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL a 174 " --> pdb=" O ASP a 195 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU a 197 " --> pdb=" O LEU a 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 7.468A pdb=" N GLU a 135 " --> pdb=" O ILE a 56 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE a 56 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU a 137 " --> pdb=" O ILE a 54 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE a 54 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL a 139 " --> pdb=" O THR a 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU a 141 " --> pdb=" O ALA a 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'a' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'b' and resid 8 through 10 removed outlier: 6.676A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 8 through 10 removed outlier: 6.676A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 173 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 100 removed outlier: 7.222A pdb=" N GLU b 135 " --> pdb=" O ILE b 56 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE b 56 " --> pdb=" O GLU b 135 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.566A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER b 166 " --> pdb=" O VAL b 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'b' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'c' and resid 39 through 40 removed outlier: 6.821A pdb=" N VAL c 39 " --> pdb=" O SER c 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'c' and resid 105 through 112 removed outlier: 6.898A pdb=" N PHE c 134 " --> pdb=" O PRO c 110 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE c 112 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY c 155 " --> pdb=" O LEU c 133 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL c 135 " --> pdb=" O PHE c 153 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE c 153 " --> pdb=" O VAL c 135 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA c 137 " --> pdb=" O THR c 151 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR c 151 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE c 139 " --> pdb=" O SER c 149 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER c 149 " --> pdb=" O PHE c 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.851A pdb=" N SER c 177 " --> pdb=" O ARG c 454 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU c 455 " --> pdb=" O GLY c 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 184 through 191 removed outlier: 3.827A pdb=" N TYR c 186 " --> pdb=" O LYS c 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL c 202 " --> pdb=" O PHE c 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 354 through 356 Processing sheet with id=AB9, first strand: chain 'c' and resid 505 through 506 removed outlier: 3.935A pdb=" N LYS c 518 " --> pdb=" O GLU c 527 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU c 527 " --> pdb=" O LYS c 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'c' and resid 558 through 559 removed outlier: 3.559A pdb=" N VAL c 559 " --> pdb=" O VAL c 571 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL c 571 " --> pdb=" O VAL c 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'c' and resid 642 through 643 removed outlier: 6.791A pdb=" N VAL c 642 " --> pdb=" O ILE c 702 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS c 687 " --> pdb=" O ASP c 704 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 667 through 671 removed outlier: 3.597A pdb=" N ARG c 668 " --> pdb=" O VAL c 660 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 676 through 677 Processing sheet with id=AC6, first strand: chain 'c' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'c' and resid 1007 through 1008 removed outlier: 3.910A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU c 737 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE c 898 " --> pdb=" O LEU c 737 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE c 723 " --> pdb=" O THR c1024 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 749 through 760 removed outlier: 3.608A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.803A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 1066 through 1068 removed outlier: 3.588A pdb=" N GLN c1066 " --> pdb=" O VAL d 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS d 420 " --> pdb=" O PHE c1068 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1133 through 1136 Processing sheet with id=AD4, first strand: chain 'd' and resid 73 through 74 removed outlier: 4.180A pdb=" N ILE d 73 " --> pdb=" O VAL d 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 93 through 102 removed outlier: 3.550A pdb=" N GLY d 93 " --> pdb=" O VAL d 319 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP d 315 " --> pdb=" O LEU d 97 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N ALA d 99 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N VAL d 313 " --> pdb=" O ALA d 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 134 through 135 Processing sheet with id=AD7, first strand: chain 'd' and resid 327 through 330 removed outlier: 3.806A pdb=" N ARG d 334 " --> pdb=" O LEU d 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 427 through 432 removed outlier: 7.710A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 497 " --> pdb=" O HIS d 544 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 611 through 612 removed outlier: 7.926A pdb=" N TYR d 612 " --> pdb=" O ARG d 636 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.673A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 902 through 904 removed outlier: 3.515A pdb=" N GLU d 903 " --> pdb=" O ILE d 911 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 1043 through 1044 removed outlier: 3.582A pdb=" N ALA d1044 " --> pdb=" O SER d1115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'd' and resid 1076 through 1079 Processing sheet with id=AE6, first strand: chain 'd' and resid 1164 through 1167 removed outlier: 4.485A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 1271 through 1273 removed outlier: 3.646A pdb=" N ALA d1271 " --> pdb=" O THR e 107 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3171 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: 11.15 Time building geometry restraints manager: 7.65 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: 8672 1.34 - 1.45: 2606 1.45 - 1.57: 14394 1.57 - 1.69: 19 1.69 - 1.81: 165 Bond restraints: 25856 Sorted by residual: bond pdb=" N ILE f 146 " pdb=" CA ILE f 146 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 6.80e+00 bond pdb=" N ILE f 150 " pdb=" CA ILE f 150 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.74e+00 bond pdb=" N GLY e 28 " pdb=" CA GLY e 28 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 bond pdb=" N GLN f 148 " pdb=" CA GLN f 148 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.70e+00 bond pdb=" N ARG f 152 " pdb=" CA ARG f 152 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 ... (remaining 25851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 33958 1.09 - 2.17: 837 2.17 - 3.26: 163 3.26 - 4.35: 82 4.35 - 5.43: 4 Bond angle restraints: 35044 Sorted by residual: angle pdb=" N ILE d1154 " pdb=" CA ILE d1154 " pdb=" C ILE d1154 " ideal model delta sigma weight residual 111.81 108.41 3.40 8.60e-01 1.35e+00 1.57e+01 angle pdb=" N ILE f 146 " pdb=" CA ILE f 146 " pdb=" C ILE f 146 " ideal model delta sigma weight residual 110.36 106.25 4.11 1.05e+00 9.07e-01 1.53e+01 angle pdb=" CA THR f 151 " pdb=" CB THR f 151 " pdb=" OG1 THR f 151 " ideal model delta sigma weight residual 109.60 104.17 5.43 1.50e+00 4.44e-01 1.31e+01 angle pdb=" CA ILE f 146 " pdb=" C ILE f 146 " pdb=" O ILE f 146 " ideal model delta sigma weight residual 121.27 118.13 3.14 1.04e+00 9.25e-01 9.14e+00 angle pdb=" CA ALA f 149 " pdb=" C ALA f 149 " pdb=" O ALA f 149 " ideal model delta sigma weight residual 120.82 117.74 3.08 1.05e+00 9.07e-01 8.60e+00 ... (remaining 35039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14823 17.95 - 35.90: 826 35.90 - 53.85: 155 53.85 - 71.80: 37 71.80 - 89.75: 5 Dihedral angle restraints: 15846 sinusoidal: 6597 harmonic: 9249 Sorted by residual: dihedral pdb=" CA LYS d1082 " pdb=" C LYS d1082 " pdb=" N ARG d1083 " pdb=" CA ARG d1083 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN d1084 " pdb=" C GLN d1084 " pdb=" N ARG d1085 " pdb=" CA ARG d1085 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ALA c1061 " pdb=" C ALA c1061 " pdb=" N GLN c1062 " pdb=" CA GLN c1062 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3163 0.043 - 0.086: 526 0.086 - 0.130: 272 0.130 - 0.173: 15 0.173 - 0.216: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CA ILE f 146 " pdb=" N ILE f 146 " pdb=" C ILE f 146 " pdb=" CB ILE f 146 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE f 150 " pdb=" N ILE f 150 " pdb=" C ILE f 150 " pdb=" CB ILE f 150 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE c1112 " pdb=" N ILE c1112 " pdb=" C ILE c1112 " pdb=" CB ILE c1112 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 3974 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG f 152 " 0.477 9.50e-02 1.11e+02 2.14e-01 2.80e+01 pdb=" NE ARG f 152 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG f 152 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG f 152 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG f 152 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP f 145 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C TRP f 145 " -0.038 2.00e-02 2.50e+03 pdb=" O TRP f 145 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE f 146 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER c 546 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO c 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO c 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO c 547 " -0.026 5.00e-02 4.00e+02 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 219 2.57 - 3.15: 22094 3.15 - 3.74: 37388 3.74 - 4.32: 51387 4.32 - 4.90: 87710 Nonbonded interactions: 198798 Sorted by model distance: nonbonded pdb=" OD1 ASP d 535 " pdb="MG MG d1503 " model vdw 1.988 2.170 nonbonded pdb=" O SER c 182 " pdb=" OH TYR c 186 " model vdw 1.997 3.040 nonbonded pdb=" OD1 ASP d 539 " pdb="MG MG d1503 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR c 354 " pdb=" OE1 GLU c 362 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU d 49 " pdb=" OG1 THR d 55 " model vdw 2.132 3.040 ... (remaining 198793 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 1 through 152 or resid 159 through 210 or (resid 211 throu \ gh 212 and (name N or name CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 1 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 62.570 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 0.040 25864 Z= 0.123 Angle : 0.469 5.432 35056 Z= 0.253 Chirality : 0.040 0.216 3977 Planarity : 0.005 0.214 4596 Dihedral : 11.779 89.752 9900 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.95 % Allowed : 5.21 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.43 (0.15), residues: 3217 helix: 1.73 (0.15), residues: 1233 sheet: -1.02 (0.29), residues: 344 loop : -0.50 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d1220 HIS 0.004 0.001 HIS d 505 PHE 0.014 0.001 PHE d 6 TYR 0.014 0.001 TYR a 168 ARG 0.003 0.000 ARG d1143 Details of bonding type rmsd hydrogen bonds : bond 0.20742 ( 1108) hydrogen bonds : angle 7.00881 ( 3171) metal coordination : bond 0.00436 ( 8) metal coordination : angle 3.15156 ( 12) covalent geometry : bond 0.00267 (25856) covalent geometry : angle 0.46527 (35044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (p0) REVERT: c 154 MET cc_start: 0.8646 (tpp) cc_final: 0.8065 (tpp) REVERT: c 322 LEU cc_start: 0.8251 (mt) cc_final: 0.7857 (mt) REVERT: c 758 ASP cc_start: 0.8372 (p0) cc_final: 0.8151 (p0) REVERT: d 70 PHE cc_start: 0.7298 (m-80) cc_final: 0.6926 (m-80) REVERT: d 155 MET cc_start: 0.5749 (tmm) cc_final: 0.5073 (tpt) REVERT: d 205 MET cc_start: 0.4380 (mmm) cc_final: 0.3706 (mmm) REVERT: d 233 GLN cc_start: 0.8270 (tt0) cc_final: 0.8069 (mt0) REVERT: d 1112 MET cc_start: 0.6352 (ptm) cc_final: 0.6139 (ppp) REVERT: e 104 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8594 (mp) outliers start: 26 outliers final: 7 residues processed: 328 average time/residue: 0.3976 time to fit residues: 202.5425 Evaluate side-chains 201 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 704 ASP Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 163 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 443 ASN c1034 HIS c1066 GLN d 329 GLN d 505 HIS d 523 GLN d 552 GLN d 606 HIS d 854 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100388 restraints weight = 45285.237| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.69 r_work: 0.3180 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25864 Z= 0.183 Angle : 0.613 9.270 35056 Z= 0.315 Chirality : 0.044 0.189 3977 Planarity : 0.004 0.040 4596 Dihedral : 6.794 69.013 3680 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.98 % Allowed : 8.66 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.39 (0.15), residues: 3217 helix: 1.65 (0.15), residues: 1260 sheet: -0.96 (0.28), residues: 366 loop : -0.55 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 938 HIS 0.009 0.001 HIS f 60 PHE 0.020 0.002 PHE d1186 TYR 0.013 0.001 TYR c 91 ARG 0.007 0.000 ARG d1143 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 1108) hydrogen bonds : angle 4.87445 ( 3171) metal coordination : bond 0.00907 ( 8) metal coordination : angle 3.81195 ( 12) covalent geometry : bond 0.00441 (25856) covalent geometry : angle 0.60954 (35044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8418 (p0) REVERT: b 184 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: b 185 GLN cc_start: 0.7729 (pm20) cc_final: 0.7399 (pm20) REVERT: c 154 MET cc_start: 0.8707 (tpp) cc_final: 0.8298 (tpp) REVERT: c 322 LEU cc_start: 0.8306 (mt) cc_final: 0.7987 (mt) REVERT: c 463 LEU cc_start: 0.8680 (pt) cc_final: 0.8450 (pp) REVERT: c 607 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8011 (mtm) REVERT: c 797 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7343 (ptm160) REVERT: c 858 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7905 (pt0) REVERT: c 978 ASP cc_start: 0.8665 (t0) cc_final: 0.8408 (t70) REVERT: c 1062 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7557 (mm-40) REVERT: d 70 PHE cc_start: 0.7862 (m-80) cc_final: 0.7240 (m-80) REVERT: d 155 MET cc_start: 0.6979 (tmm) cc_final: 0.5568 (tpt) REVERT: d 205 MET cc_start: 0.5148 (mmm) cc_final: 0.4485 (mtp) REVERT: d 233 GLN cc_start: 0.8260 (tt0) cc_final: 0.7753 (mt0) REVERT: d 787 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: d 1083 ARG cc_start: 0.5554 (mmt180) cc_final: 0.4951 (mmp80) REVERT: d 1112 MET cc_start: 0.7246 (ptm) cc_final: 0.6365 (ppp) REVERT: d 1277 GLU cc_start: 0.8444 (tp30) cc_final: 0.8022 (mt-10) REVERT: f 25 ASP cc_start: 0.6843 (t0) cc_final: 0.6440 (t0) outliers start: 54 outliers final: 24 residues processed: 253 average time/residue: 0.3720 time to fit residues: 151.2130 Evaluate side-chains 215 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 399 VAL Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 724 MET Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 925 LEU Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 308 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 240 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 185 GLN b 5 GLN c 443 ASN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100117 restraints weight = 45265.919| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.80 r_work: 0.3158 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25864 Z= 0.183 Angle : 0.578 7.656 35056 Z= 0.296 Chirality : 0.042 0.251 3977 Planarity : 0.004 0.037 4596 Dihedral : 6.759 73.986 3674 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.72 % Allowed : 10.72 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.30 (0.15), residues: 3217 helix: 1.53 (0.15), residues: 1266 sheet: -0.81 (0.27), residues: 369 loop : -0.61 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 938 HIS 0.014 0.001 HIS f 166 PHE 0.016 0.001 PHE f 274 TYR 0.019 0.001 TYR d 915 ARG 0.008 0.000 ARG d1143 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1108) hydrogen bonds : angle 4.62100 ( 3171) metal coordination : bond 0.00898 ( 8) metal coordination : angle 3.40786 ( 12) covalent geometry : bond 0.00443 (25856) covalent geometry : angle 0.57471 (35044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 2.741 Fit side-chains revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8382 (p0) REVERT: c 154 MET cc_start: 0.8706 (tpp) cc_final: 0.8386 (tpp) REVERT: c 322 LEU cc_start: 0.8273 (mt) cc_final: 0.7992 (mt) REVERT: c 355 MET cc_start: 0.5618 (tmm) cc_final: 0.4649 (tmm) REVERT: c 463 LEU cc_start: 0.8629 (pt) cc_final: 0.8377 (pp) REVERT: c 558 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7369 (ttm-80) REVERT: c 858 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7947 (pt0) REVERT: c 1062 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7528 (mm-40) REVERT: c 1087 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7881 (mt-10) REVERT: d 70 PHE cc_start: 0.7891 (m-80) cc_final: 0.7285 (m-80) REVERT: d 155 MET cc_start: 0.7037 (tmm) cc_final: 0.5627 (tpt) REVERT: d 205 MET cc_start: 0.4866 (mmm) cc_final: 0.4227 (mtp) REVERT: d 233 GLN cc_start: 0.8506 (tt0) cc_final: 0.7910 (mt0) REVERT: d 787 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: d 1083 ARG cc_start: 0.5555 (mmt180) cc_final: 0.5018 (mmp80) REVERT: d 1277 GLU cc_start: 0.8481 (tp30) cc_final: 0.8066 (mt-10) REVERT: f 25 ASP cc_start: 0.6836 (t0) cc_final: 0.6476 (t0) outliers start: 74 outliers final: 41 residues processed: 259 average time/residue: 0.3384 time to fit residues: 145.1320 Evaluate side-chains 226 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 342 ILE Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 408 ASP Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 559 VAL Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 789 ILE Chi-restraints excluded: chain c residue 866 ASN Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 925 LEU Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 137 optimal weight: 8.9990 chunk 226 optimal weight: 0.0770 chunk 143 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 277 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 104 optimal weight: 0.0770 overall best weight: 1.1698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 443 ASN d 103 HIS d 525 HIS d 606 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100941 restraints weight = 45238.410| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.72 r_work: 0.3193 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25864 Z= 0.125 Angle : 0.524 9.867 35056 Z= 0.269 Chirality : 0.041 0.212 3977 Planarity : 0.004 0.046 4596 Dihedral : 6.679 78.638 3674 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.20 % Allowed : 12.22 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.43 (0.15), residues: 3217 helix: 1.68 (0.15), residues: 1260 sheet: -0.90 (0.27), residues: 371 loop : -0.53 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 938 HIS 0.011 0.001 HIS f 166 PHE 0.014 0.001 PHE d 268 TYR 0.015 0.001 TYR c 91 ARG 0.007 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 1108) hydrogen bonds : angle 4.38310 ( 3171) metal coordination : bond 0.00612 ( 8) metal coordination : angle 2.81011 ( 12) covalent geometry : bond 0.00291 (25856) covalent geometry : angle 0.52120 (35044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 2.963 Fit side-chains revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8309 (p0) REVERT: c 107 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6906 (p90) REVERT: c 154 MET cc_start: 0.8673 (tpp) cc_final: 0.8174 (tpp) REVERT: c 322 LEU cc_start: 0.8234 (mt) cc_final: 0.7979 (mt) REVERT: c 355 MET cc_start: 0.5910 (tmm) cc_final: 0.5605 (tmm) REVERT: c 463 LEU cc_start: 0.8631 (pt) cc_final: 0.8353 (pp) REVERT: c 470 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8012 (tt) REVERT: c 558 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7267 (ttm-80) REVERT: c 564 LYS cc_start: 0.7831 (tttt) cc_final: 0.7371 (pttm) REVERT: c 607 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7890 (mtm) REVERT: c 661 MET cc_start: 0.8526 (tpt) cc_final: 0.8311 (tpt) REVERT: c 858 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7902 (pt0) REVERT: c 1062 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7458 (mm-40) REVERT: d 70 PHE cc_start: 0.7877 (m-80) cc_final: 0.7261 (m-10) REVERT: d 155 MET cc_start: 0.6988 (tmm) cc_final: 0.5564 (tpt) REVERT: d 205 MET cc_start: 0.4657 (mmm) cc_final: 0.4032 (mtp) REVERT: d 233 GLN cc_start: 0.8520 (tt0) cc_final: 0.8158 (mt0) REVERT: d 312 MET cc_start: 0.8833 (mmm) cc_final: 0.8300 (mtp) REVERT: d 787 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: d 1083 ARG cc_start: 0.5515 (mmt180) cc_final: 0.4974 (mmp80) REVERT: d 1112 MET cc_start: 0.7423 (ptm) cc_final: 0.6882 (ppp) REVERT: d 1277 GLU cc_start: 0.8478 (tp30) cc_final: 0.8178 (mt-10) REVERT: f 25 ASP cc_start: 0.7013 (t0) cc_final: 0.6608 (t0) outliers start: 60 outliers final: 35 residues processed: 252 average time/residue: 0.3475 time to fit residues: 142.5647 Evaluate side-chains 226 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 143 MET Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 646 ILE Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 80 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 317 optimal weight: 0.0970 chunk 238 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 GLN c 443 ASN e 65 ASN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.140336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101257 restraints weight = 45207.790| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.69 r_work: 0.3206 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25864 Z= 0.114 Angle : 0.511 7.240 35056 Z= 0.262 Chirality : 0.040 0.141 3977 Planarity : 0.004 0.037 4596 Dihedral : 6.630 81.091 3674 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.39 % Allowed : 13.21 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.48 (0.15), residues: 3217 helix: 1.71 (0.15), residues: 1260 sheet: -0.86 (0.27), residues: 377 loop : -0.49 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 938 HIS 0.010 0.001 HIS f 60 PHE 0.014 0.001 PHE c 214 TYR 0.022 0.001 TYR c 657 ARG 0.007 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1108) hydrogen bonds : angle 4.26660 ( 3171) metal coordination : bond 0.00521 ( 8) metal coordination : angle 2.60549 ( 12) covalent geometry : bond 0.00263 (25856) covalent geometry : angle 0.50872 (35044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8293 (p0) REVERT: b 184 GLU cc_start: 0.7987 (mp0) cc_final: 0.7717 (tt0) REVERT: c 107 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.6899 (p90) REVERT: c 154 MET cc_start: 0.8698 (tpp) cc_final: 0.8412 (tpp) REVERT: c 355 MET cc_start: 0.6007 (tmm) cc_final: 0.5657 (tmm) REVERT: c 463 LEU cc_start: 0.8622 (pt) cc_final: 0.8343 (pp) REVERT: c 470 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8019 (tt) REVERT: c 564 LYS cc_start: 0.7752 (tttt) cc_final: 0.7348 (pttm) REVERT: c 607 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7866 (mtm) REVERT: c 661 MET cc_start: 0.8512 (tpt) cc_final: 0.8298 (tpt) REVERT: c 858 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7888 (pt0) REVERT: d 70 PHE cc_start: 0.7906 (m-80) cc_final: 0.7289 (m-10) REVERT: d 155 MET cc_start: 0.6979 (tmm) cc_final: 0.5606 (tpt) REVERT: d 205 MET cc_start: 0.4678 (mmm) cc_final: 0.4036 (mtp) REVERT: d 233 GLN cc_start: 0.8535 (tt0) cc_final: 0.8147 (mt0) REVERT: d 312 MET cc_start: 0.8797 (mmm) cc_final: 0.8168 (mtp) REVERT: d 787 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: d 1083 ARG cc_start: 0.5489 (mmt180) cc_final: 0.4962 (mmp80) REVERT: d 1112 MET cc_start: 0.7350 (ptm) cc_final: 0.6740 (ptm) REVERT: d 1277 GLU cc_start: 0.8446 (tp30) cc_final: 0.8221 (mt-10) REVERT: f 25 ASP cc_start: 0.6847 (t0) cc_final: 0.6529 (t70) outliers start: 65 outliers final: 39 residues processed: 243 average time/residue: 0.3457 time to fit residues: 138.4904 Evaluate side-chains 231 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 646 ILE Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 167 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 56 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 305 optimal weight: 7.9990 chunk 287 optimal weight: 0.3980 chunk 18 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 443 ASN ** f 120 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.137930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.098909 restraints weight = 45072.816| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.78 r_work: 0.3154 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25864 Z= 0.187 Angle : 0.553 7.242 35056 Z= 0.284 Chirality : 0.042 0.171 3977 Planarity : 0.004 0.039 4596 Dihedral : 6.701 80.776 3673 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.50 % Allowed : 14.13 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.38 (0.15), residues: 3217 helix: 1.63 (0.15), residues: 1265 sheet: -0.86 (0.26), residues: 387 loop : -0.57 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 938 HIS 0.015 0.001 HIS f 60 PHE 0.014 0.001 PHE c 214 TYR 0.015 0.001 TYR c 91 ARG 0.007 0.000 ARG d 459 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 1108) hydrogen bonds : angle 4.32288 ( 3171) metal coordination : bond 0.00892 ( 8) metal coordination : angle 2.87850 ( 12) covalent geometry : bond 0.00457 (25856) covalent geometry : angle 0.55095 (35044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8356 (p0) REVERT: b 184 GLU cc_start: 0.7992 (mp0) cc_final: 0.7694 (tt0) REVERT: c 154 MET cc_start: 0.8730 (tpp) cc_final: 0.8396 (tpp) REVERT: c 355 MET cc_start: 0.6055 (tmm) cc_final: 0.5703 (tmm) REVERT: c 463 LEU cc_start: 0.8642 (pt) cc_final: 0.8360 (pp) REVERT: c 470 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8042 (tt) REVERT: c 564 LYS cc_start: 0.7741 (tttt) cc_final: 0.7296 (pttm) REVERT: c 607 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7940 (mtm) REVERT: c 661 MET cc_start: 0.8560 (tpt) cc_final: 0.8333 (tpt) REVERT: c 858 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7934 (pt0) REVERT: d 70 PHE cc_start: 0.7946 (m-80) cc_final: 0.7322 (m-10) REVERT: d 155 MET cc_start: 0.7046 (tmm) cc_final: 0.5550 (tpt) REVERT: d 205 MET cc_start: 0.4717 (mmm) cc_final: 0.4103 (mtp) REVERT: d 233 GLN cc_start: 0.8561 (tt0) cc_final: 0.7903 (mt0) REVERT: d 296 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6812 (tp) REVERT: d 400 LYS cc_start: 0.8168 (tttt) cc_final: 0.7861 (ttmt) REVERT: d 787 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: d 1083 ARG cc_start: 0.5592 (mmt180) cc_final: 0.5030 (mmp80) REVERT: d 1112 MET cc_start: 0.7352 (ptm) cc_final: 0.6780 (ptm) REVERT: d 1277 GLU cc_start: 0.8465 (tp30) cc_final: 0.8200 (mt-10) REVERT: f 25 ASP cc_start: 0.6788 (t0) cc_final: 0.6431 (t70) outliers start: 68 outliers final: 50 residues processed: 243 average time/residue: 0.3357 time to fit residues: 137.3326 Evaluate side-chains 239 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 559 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 167 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 233 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 307 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 88 GLN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103112 restraints weight = 45606.495| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.85 r_work: 0.3137 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25864 Z= 0.176 Angle : 0.545 8.330 35056 Z= 0.279 Chirality : 0.042 0.307 3977 Planarity : 0.004 0.040 4596 Dihedral : 6.718 80.952 3673 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.97 % Allowed : 14.20 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.35 (0.15), residues: 3217 helix: 1.63 (0.15), residues: 1263 sheet: -0.86 (0.27), residues: 378 loop : -0.61 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 938 HIS 0.010 0.001 HIS f 166 PHE 0.013 0.001 PHE d 268 TYR 0.013 0.001 TYR c 731 ARG 0.007 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 1108) hydrogen bonds : angle 4.30034 ( 3171) metal coordination : bond 0.00883 ( 8) metal coordination : angle 2.84049 ( 12) covalent geometry : bond 0.00427 (25856) covalent geometry : angle 0.54229 (35044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 189 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8225 (p0) REVERT: b 184 GLU cc_start: 0.7863 (mp0) cc_final: 0.7584 (tt0) REVERT: c 154 MET cc_start: 0.8705 (tpp) cc_final: 0.8360 (tpp) REVERT: c 355 MET cc_start: 0.6112 (tmm) cc_final: 0.5775 (tmm) REVERT: c 463 LEU cc_start: 0.8616 (pt) cc_final: 0.8378 (pp) REVERT: c 470 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (tt) REVERT: c 564 LYS cc_start: 0.7662 (tttt) cc_final: 0.7288 (pttm) REVERT: c 607 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: c 858 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7860 (pt0) REVERT: d 70 PHE cc_start: 0.7939 (m-80) cc_final: 0.7490 (m-80) REVERT: d 155 MET cc_start: 0.6897 (tmm) cc_final: 0.5533 (tpt) REVERT: d 205 MET cc_start: 0.4694 (mmm) cc_final: 0.4047 (mtp) REVERT: d 233 GLN cc_start: 0.8532 (tt0) cc_final: 0.7858 (mt0) REVERT: d 296 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6915 (tp) REVERT: d 400 LYS cc_start: 0.7954 (tttt) cc_final: 0.7645 (ttmt) REVERT: d 493 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: d 787 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: d 1083 ARG cc_start: 0.5523 (mmt180) cc_final: 0.5003 (mmp80) REVERT: d 1112 MET cc_start: 0.7305 (ptm) cc_final: 0.6760 (ptm) REVERT: f 25 ASP cc_start: 0.6758 (t0) cc_final: 0.6433 (t70) outliers start: 81 outliers final: 55 residues processed: 252 average time/residue: 0.3266 time to fit residues: 137.3476 Evaluate side-chains 242 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 433 THR Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 559 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 865 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 493 GLU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1098 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 167 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 270 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 60 HIS ** f 120 ASN ** 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 = 0.3979 r_free = 0.3979 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098578 restraints weight = 44986.080| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.83 r_work: 0.3149 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25864 Z= 0.181 Angle : 0.558 12.644 35056 Z= 0.284 Chirality : 0.042 0.363 3977 Planarity : 0.004 0.041 4596 Dihedral : 6.739 81.127 3673 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.72 % Allowed : 15.34 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.32 (0.15), residues: 3217 helix: 1.62 (0.15), residues: 1266 sheet: -0.87 (0.27), residues: 378 loop : -0.64 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 938 HIS 0.011 0.001 HIS f 60 PHE 0.013 0.001 PHE d 268 TYR 0.016 0.001 TYR c 91 ARG 0.008 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1108) hydrogen bonds : angle 4.31302 ( 3171) metal coordination : bond 0.00895 ( 8) metal coordination : angle 2.86691 ( 12) covalent geometry : bond 0.00440 (25856) covalent geometry : angle 0.55602 (35044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8319 (p0) REVERT: b 184 GLU cc_start: 0.8066 (mp0) cc_final: 0.7624 (tt0) REVERT: c 154 MET cc_start: 0.8770 (tpp) cc_final: 0.8437 (tpp) REVERT: c 355 MET cc_start: 0.6135 (tmm) cc_final: 0.5769 (tmm) REVERT: c 463 LEU cc_start: 0.8648 (pt) cc_final: 0.8368 (pp) REVERT: c 470 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8012 (tt) REVERT: c 564 LYS cc_start: 0.7667 (tttt) cc_final: 0.7234 (pttm) REVERT: c 607 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7951 (mtm) REVERT: c 858 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7937 (pt0) REVERT: d 70 PHE cc_start: 0.7961 (m-80) cc_final: 0.7480 (m-80) REVERT: d 155 MET cc_start: 0.6904 (tmm) cc_final: 0.5566 (tpt) REVERT: d 205 MET cc_start: 0.4691 (mmm) cc_final: 0.4047 (mtp) REVERT: d 233 GLN cc_start: 0.8606 (tt0) cc_final: 0.8310 (mt0) REVERT: d 296 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6993 (tp) REVERT: d 312 MET cc_start: 0.8895 (mmm) cc_final: 0.8033 (mmt) REVERT: d 400 LYS cc_start: 0.8123 (tttt) cc_final: 0.7822 (ttmt) REVERT: d 493 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: d 787 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: d 1083 ARG cc_start: 0.5636 (mmt180) cc_final: 0.5023 (mmp80) REVERT: d 1112 MET cc_start: 0.7399 (ptm) cc_final: 0.6843 (ptm) REVERT: e 42 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8416 (mt-10) REVERT: f 25 ASP cc_start: 0.6801 (t0) cc_final: 0.6432 (t70) outliers start: 74 outliers final: 55 residues processed: 241 average time/residue: 0.3382 time to fit residues: 135.8509 Evaluate side-chains 240 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 433 THR Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 559 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 865 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 493 GLU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1098 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 167 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 57 optimal weight: 10.0000 chunk 281 optimal weight: 0.0050 chunk 299 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 195 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 264 optimal weight: 20.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100563 restraints weight = 45134.277| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.74 r_work: 0.3191 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25864 Z= 0.106 Angle : 0.516 11.877 35056 Z= 0.262 Chirality : 0.040 0.324 3977 Planarity : 0.004 0.042 4596 Dihedral : 6.641 83.183 3673 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.09 % Allowed : 15.63 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.49 (0.15), residues: 3217 helix: 1.75 (0.15), residues: 1262 sheet: -0.89 (0.28), residues: 375 loop : -0.50 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 938 HIS 0.027 0.001 HIS f 60 PHE 0.011 0.001 PHE d 268 TYR 0.018 0.001 TYR c 91 ARG 0.008 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1108) hydrogen bonds : angle 4.19763 ( 3171) metal coordination : bond 0.00506 ( 8) metal coordination : angle 2.50652 ( 12) covalent geometry : bond 0.00243 (25856) covalent geometry : angle 0.51381 (35044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8318 (p0) REVERT: b 184 GLU cc_start: 0.8058 (mp0) cc_final: 0.7540 (tt0) REVERT: c 107 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7244 (p90) REVERT: c 154 MET cc_start: 0.8696 (tpp) cc_final: 0.8425 (tpp) REVERT: c 463 LEU cc_start: 0.8614 (pt) cc_final: 0.8358 (pp) REVERT: c 470 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (tt) REVERT: c 564 LYS cc_start: 0.7501 (tttt) cc_final: 0.7123 (pttm) REVERT: c 607 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7790 (mtm) REVERT: c 858 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7895 (pt0) REVERT: d 70 PHE cc_start: 0.7939 (m-80) cc_final: 0.7329 (m-10) REVERT: d 155 MET cc_start: 0.7052 (tmm) cc_final: 0.5617 (tpt) REVERT: d 205 MET cc_start: 0.4714 (mmm) cc_final: 0.4088 (mtp) REVERT: d 233 GLN cc_start: 0.8506 (tt0) cc_final: 0.8063 (mt0) REVERT: d 296 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6811 (tp) REVERT: d 400 LYS cc_start: 0.8107 (tttt) cc_final: 0.7887 (ttmt) REVERT: d 787 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: d 1083 ARG cc_start: 0.5620 (mmt180) cc_final: 0.5047 (mmp80) REVERT: d 1112 MET cc_start: 0.7366 (ptm) cc_final: 0.6801 (ptm) REVERT: e 42 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8318 (mt-10) REVERT: e 66 ASP cc_start: 0.8942 (t0) cc_final: 0.8718 (t0) REVERT: f 25 ASP cc_start: 0.6875 (t0) cc_final: 0.6545 (t70) outliers start: 57 outliers final: 40 residues processed: 246 average time/residue: 0.3196 time to fit residues: 131.3927 Evaluate side-chains 228 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 672 MET Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 300 optimal weight: 6.9990 chunk 111 optimal weight: 0.0020 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 291 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 61 HIS ** f 120 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.140355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101576 restraints weight = 45115.702| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.63 r_work: 0.3215 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25864 Z= 0.102 Angle : 0.519 11.071 35056 Z= 0.262 Chirality : 0.040 0.304 3977 Planarity : 0.004 0.042 4596 Dihedral : 6.582 85.090 3673 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 16.11 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.59 (0.15), residues: 3217 helix: 1.81 (0.15), residues: 1266 sheet: -0.81 (0.28), residues: 375 loop : -0.45 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 938 HIS 0.009 0.001 HIS f 252 PHE 0.012 0.001 PHE d 651 TYR 0.010 0.001 TYR d 749 ARG 0.009 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1108) hydrogen bonds : angle 4.14437 ( 3171) metal coordination : bond 0.00427 ( 8) metal coordination : angle 2.28205 ( 12) covalent geometry : bond 0.00232 (25856) covalent geometry : angle 0.51766 (35044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (p0) REVERT: b 60 LEU cc_start: 0.7082 (tp) cc_final: 0.6510 (mt) REVERT: b 184 GLU cc_start: 0.8022 (mp0) cc_final: 0.7793 (pm20) REVERT: c 154 MET cc_start: 0.8672 (tpp) cc_final: 0.8040 (tpp) REVERT: c 211 TRP cc_start: 0.7162 (m-10) cc_final: 0.6944 (m-10) REVERT: c 355 MET cc_start: 0.7219 (tmm) cc_final: 0.6916 (tmm) REVERT: c 463 LEU cc_start: 0.8635 (pt) cc_final: 0.8380 (pp) REVERT: c 467 ARG cc_start: 0.6218 (mmt-90) cc_final: 0.5970 (tpp80) REVERT: c 470 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (tt) REVERT: c 564 LYS cc_start: 0.7440 (tttt) cc_final: 0.7100 (pttm) REVERT: c 607 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7560 (mtm) REVERT: c 858 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7866 (pt0) REVERT: d 70 PHE cc_start: 0.7926 (m-80) cc_final: 0.7315 (m-10) REVERT: d 205 MET cc_start: 0.4661 (mmm) cc_final: 0.4025 (mtp) REVERT: d 233 GLN cc_start: 0.8516 (tt0) cc_final: 0.8239 (mt0) REVERT: d 296 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6454 (mt) REVERT: d 400 LYS cc_start: 0.8121 (tttt) cc_final: 0.7913 (ttmt) REVERT: d 787 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: d 1083 ARG cc_start: 0.5578 (mmt180) cc_final: 0.5029 (mmp80) REVERT: d 1112 MET cc_start: 0.7337 (ptm) cc_final: 0.6772 (ptm) REVERT: e 66 ASP cc_start: 0.8915 (t0) cc_final: 0.8709 (t0) REVERT: f 25 ASP cc_start: 0.6795 (t0) cc_final: 0.6459 (t70) REVERT: f 154 MET cc_start: 0.8003 (ttm) cc_final: 0.7748 (tmm) outliers start: 54 outliers final: 38 residues processed: 234 average time/residue: 0.3291 time to fit residues: 127.2934 Evaluate side-chains 231 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 672 MET Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 971 ILE Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 296 LEU Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 74 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 218 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 177 optimal weight: 40.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 65 ASN e 88 GLN ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.138003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099200 restraints weight = 45024.340| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.77 r_work: 0.3158 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25864 Z= 0.172 Angle : 0.563 10.490 35056 Z= 0.284 Chirality : 0.042 0.297 3977 Planarity : 0.004 0.046 4596 Dihedral : 6.581 84.082 3671 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.02 % Allowed : 15.96 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.46 (0.15), residues: 3217 helix: 1.72 (0.15), residues: 1262 sheet: -0.71 (0.28), residues: 375 loop : -0.57 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 938 HIS 0.008 0.001 HIS f 252 PHE 0.013 0.001 PHE d 673 TYR 0.018 0.001 TYR c 91 ARG 0.008 0.000 ARG d 762 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 1108) hydrogen bonds : angle 4.22030 ( 3171) metal coordination : bond 0.00811 ( 8) metal coordination : angle 2.50790 ( 12) covalent geometry : bond 0.00419 (25856) covalent geometry : angle 0.56074 (35044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14690.19 seconds wall clock time: 254 minutes 5.16 seconds (15245.16 seconds total)