Starting phenix.real_space_refine on Tue Sep 15 10:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844.map" model { file = "/net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aoh_11844/09_2026/7aoh_11844_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.271 sd= 1.084 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 4 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 174 5.16 5 C 25126 2.51 5 N 6581 2.21 5 O 7533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39496 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 10145 Classifications: {'peptide': 1263} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1218} Chain: "B" Number of atoms: 9130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9130 Classifications: {'peptide': 1134} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1081} Chain breaks: 2 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1233 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "I" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6234 Classifications: {'peptide': 746} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 720} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "N" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 575 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "S" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "T" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 800 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "Y" Number of atoms: 4817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4817 Classifications: {'peptide': 597} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 585} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 89.032 104.854 79.660 1.00 62.50 S ATOM 382 SG CYS A 52 92.772 104.997 79.002 1.00 57.84 S ATOM 434 SG CYS A 59 91.063 101.626 79.662 1.00 57.14 S ATOM 694 SG CYS A 90 79.122 95.222 126.739 1.00 89.60 S ATOM 718 SG CYS A 93 81.639 98.199 127.866 1.00 91.77 S ATOM 1016 SG CYS A 130 81.173 95.898 130.238 1.00 96.50 S ATOM 18684 SG CYS B1087 100.722 103.718 92.972 1.00 48.14 S ATOM 18707 SG CYS B1090 97.253 102.356 93.831 1.00 50.62 S ATOM 18796 SG CYS B1103 97.549 105.208 91.587 1.00 50.54 S ATOM 18821 SG CYS B1106 98.438 105.716 95.274 1.00 52.12 S ATOM 31609 SG CYS J 7 91.267 39.239 44.615 1.00 41.61 S ATOM 31628 SG CYS J 10 94.265 38.082 42.468 1.00 42.50 S ATOM 31865 SG CYS J 39 93.262 36.299 45.779 1.00 43.36 S ATOM 31871 SG CYS J 40 91.353 36.079 42.416 1.00 44.10 S Time building chain proxies: 7.63, per 1000 atoms: 0.19 Number of scatterers: 39496 At special positions: 0 Unit cell: (161, 156.325, 161.821, 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 4 29.99 S 174 16.00 P 77 15.00 Mg 1 11.99 O 7533 8.00 N 6581 7.00 C 25126 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: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " Number of angles added : 15 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8952 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 54 sheets defined 45.2% alpha, 17.9% beta 31 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.591A pdb=" N ARG A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 4.029A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 267 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 349 through 352 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 406 through 413 removed outlier: 4.896A pdb=" N ASN A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.511A pdb=" N ARG A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.097A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 529 through 534 removed outlier: 4.024A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.752A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 removed outlier: 4.307A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 751 " --> pdb=" O CYS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.830A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.601A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.595A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.468A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.613A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.398A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1170 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 3.937A pdb=" N ASP A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.744A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.645A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 277 Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 303 through 314 removed outlier: 3.581A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.617A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 361 through 393 removed outlier: 3.541A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 3.909A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.931A pdb=" N LEU B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.913A pdb=" N TYR B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 604 through 611 removed outlier: 4.252A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.510A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.622A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.705A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.849A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 916 through 923 removed outlier: 4.192A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.601A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 Processing helix chain 'B' and resid 981 through 991 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.601A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 58 through 59 No H-bonds generated for 'chain 'C' and resid 58 through 59' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.652A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.662A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.849A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.559A pdb=" N ARG C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.831A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.538A pdb=" N TYR F 153 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.984A pdb=" N GLY G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 21 removed outlier: 3.674A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Proline residue: I 13 - end of helix removed outlier: 4.011A pdb=" N ASP I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 Processing helix chain 'I' and resid 37 through 45 removed outlier: 3.877A pdb=" N PHE I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE I 42 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN I 43 " --> pdb=" O PHE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 65 Processing helix chain 'I' and resid 69 through 80 removed outlier: 4.223A pdb=" N ALA I 75 " --> pdb=" O GLN I 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.731A pdb=" N THR I 108 " --> pdb=" O THR I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.621A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.763A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 4.068A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 353 Processing helix chain 'I' and resid 370 through 374 removed outlier: 3.650A pdb=" N ASN I 374 " --> pdb=" O PRO I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 404 removed outlier: 4.006A pdb=" N VAL I 404 " --> pdb=" O SER I 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 401 through 404' Processing helix chain 'I' and resid 405 through 421 removed outlier: 4.656A pdb=" N PHE I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 428 through 446 Processing helix chain 'I' and resid 446 through 454 Processing helix chain 'I' and resid 454 through 459 Processing helix chain 'I' and resid 482 through 501 Processing helix chain 'I' and resid 503 through 514 removed outlier: 4.020A pdb=" N ILE I 507 " --> pdb=" O SER I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 557 Processing helix chain 'I' and resid 561 through 581 removed outlier: 3.721A pdb=" N ILE I 581 " --> pdb=" O LYS I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 3.912A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 removed outlier: 3.500A pdb=" N VAL I 727 " --> pdb=" O ASP I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.670A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.893A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 24 through 32 removed outlier: 3.735A pdb=" N GLN S 30 " --> pdb=" O GLU S 26 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR S 31 " --> pdb=" O LEU S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 51 Processing helix chain 'S' and resid 69 through 79 removed outlier: 4.526A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 85 removed outlier: 3.640A pdb=" N ASN S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 removed outlier: 3.976A pdb=" N LYS S 108 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.684A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 139 Processing helix chain 'Y' and resid 5 through 16 Processing helix chain 'Y' and resid 32 through 45 Processing helix chain 'Y' and resid 60 through 71 removed outlier: 3.565A pdb=" N THR Y 64 " --> pdb=" O GLY Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 75 Processing helix chain 'Y' and resid 86 through 90 Processing helix chain 'Y' and resid 92 through 102 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 3.760A pdb=" N THR Y 106 " --> pdb=" O PRO Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 118 through 128 Processing helix chain 'Y' and resid 142 through 151 removed outlier: 3.695A pdb=" N PHE Y 146 " --> pdb=" O GLU Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 175 removed outlier: 3.986A pdb=" N LYS Y 170 " --> pdb=" O ASN Y 166 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 3.851A pdb=" N THR Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 227 Processing helix chain 'Y' and resid 264 through 281 Processing helix chain 'Y' and resid 287 through 296 Processing helix chain 'Y' and resid 322 through 328 Processing helix chain 'Y' and resid 334 through 342 Processing helix chain 'Y' and resid 351 through 365 Processing helix chain 'Y' and resid 365 through 378 Processing helix chain 'Y' and resid 392 through 405 removed outlier: 4.009A pdb=" N ILE Y 396 " --> pdb=" O SER Y 392 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 418 through 427 Processing helix chain 'Y' and resid 466 through 479 Processing helix chain 'Y' and resid 508 through 534 removed outlier: 3.904A pdb=" N GLN Y 526 " --> pdb=" O LYS Y 522 " (cutoff:3.500A) Processing helix chain 'Y' and resid 535 through 543 Processing helix chain 'Y' and resid 554 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.213A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 4.304A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 4.042A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.506A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.469A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 360 Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.443A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB5, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB6, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB7, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB8, first strand: chain 'A' and resid 1006 through 1012 Processing sheet with id=AB9, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.752A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.752A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE G 50 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE G 48 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR G 75 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 5.208A pdb=" N LYS B 53 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 70 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 52 through 59 removed outlier: 5.208A pdb=" N LYS B 53 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 70 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 360 removed outlier: 5.446A pdb=" N ARG B 358 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.798A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC9, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.680A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.719A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.719A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD4, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.580A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 823 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 1085 through 1087 Processing sheet with id=AD7, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.571A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AE1, first strand: chain 'C' and resid 37 through 43 removed outlier: 4.998A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.522A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.598A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 35 through 40 removed outlier: 6.227A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.401A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 90 removed outlier: 7.553A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 114 through 118 Processing sheet with id=AE8, first strand: chain 'I' and resid 84 through 89 removed outlier: 3.716A pdb=" N ILE Y 576 " --> pdb=" O GLN I 86 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY Y 598 " --> pdb=" O ARG Y 602 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG Y 602 " --> pdb=" O GLY Y 598 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 84 through 89 removed outlier: 3.716A pdb=" N ILE Y 576 " --> pdb=" O GLN I 86 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N LEU Y 627 " --> pdb=" O ASN Y 580 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP Y 582 " --> pdb=" O LEU Y 627 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.111A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.768A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 209 through 217 removed outlier: 3.639A pdb=" N VAL I 209 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AF5, first strand: chain 'I' and resid 656 through 660 Processing sheet with id=AF6, first strand: chain 'I' and resid 668 through 670 Processing sheet with id=AF7, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF8, first strand: chain 'Y' and resid 109 through 113 removed outlier: 8.642A pdb=" N ILE Y 110 " --> pdb=" O TRP Y 79 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE Y 81 " --> pdb=" O ILE Y 110 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE Y 112 " --> pdb=" O ILE Y 81 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU Y 83 " --> pdb=" O ILE Y 112 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA Y 80 " --> pdb=" O CYS Y 137 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE Y 139 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE Y 82 " --> pdb=" O ILE Y 139 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP Y 141 " --> pdb=" O ILE Y 82 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU Y 84 " --> pdb=" O ASP Y 141 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE Y 136 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE Y 180 " --> pdb=" O ILE Y 136 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL Y 138 " --> pdb=" O ILE Y 180 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU Y 182 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE Y 140 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER Y 232 " --> pdb=" O SER Y 50 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU Y 52 " --> pdb=" O SER Y 232 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE Y 234 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE Y 54 " --> pdb=" O ILE Y 234 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 253 through 262 removed outlier: 6.807A pdb=" N ASN Y 456 " --> pdb=" O ASN Y 494 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS Y 496 " --> pdb=" O ASN Y 456 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE Y 458 " --> pdb=" O HIS Y 496 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE Y 498 " --> pdb=" O ILE Y 458 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE Y 460 " --> pdb=" O ILE Y 498 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA Y 500 " --> pdb=" O ILE Y 460 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS Y 381 " --> pdb=" O ASP Y 457 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE Y 459 " --> pdb=" O LYS Y 381 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU Y 383 " --> pdb=" O PHE Y 459 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N CYS Y 382 " --> pdb=" O CYS Y 440 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE Y 442 " --> pdb=" O CYS Y 382 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL Y 384 " --> pdb=" O PHE Y 442 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE Y 409 " --> pdb=" O VAL Y 441 " (cutoff:3.500A) 1735 hydrogen bonds defined for protein. 4779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 11.08 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11755 1.33 - 1.45: 6395 1.45 - 1.57: 21865 1.57 - 1.69: 150 1.69 - 1.81: 277 Bond restraints: 40442 Sorted by residual: bond pdb=" C1' DC N 54 " pdb=" N1 DC N 54 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.05e+01 bond pdb=" C1' DC N 7 " pdb=" N1 DC N 7 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" C1' DT N 56 " pdb=" N1 DT N 56 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" C1' DC N 2 " pdb=" N1 DC N 2 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.56e+01 bond pdb=" C1' DT T 48 " pdb=" N1 DT T 48 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.53e+01 ... (remaining 40437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 54051 2.16 - 4.32: 787 4.32 - 6.48: 120 6.48 - 8.64: 9 8.64 - 10.80: 3 Bond angle restraints: 54970 Sorted by residual: angle pdb=" C3' A P 4 " pdb=" O3' A P 4 " pdb=" P U P 5 " ideal model delta sigma weight residual 119.70 125.69 -5.99 1.20e+00 6.94e-01 2.49e+01 angle pdb=" O4' DT T 49 " pdb=" C4' DT T 49 " pdb=" C3' DT T 49 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O5' DT T 48 " pdb=" C5' DT T 48 " pdb=" C4' DT T 48 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" N3 DT N 8 " pdb=" C4 DT N 8 " pdb=" O4 DT N 8 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O4' DT T 48 " pdb=" C1' DT T 48 " pdb=" N1 DT T 48 " ideal model delta sigma weight residual 108.00 110.99 -2.99 7.00e-01 2.04e+00 1.82e+01 ... (remaining 54965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 23550 30.26 - 60.51: 744 60.51 - 90.77: 35 90.77 - 121.02: 0 121.02 - 151.28: 3 Dihedral angle restraints: 24332 sinusoidal: 10493 harmonic: 13839 Sorted by residual: dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 149.30 30.70 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL G 62 " pdb=" C VAL G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER Y 407 " pdb=" C SER Y 407 " pdb=" N ASN Y 408 " pdb=" CA ASN Y 408 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 24329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4085 0.039 - 0.079: 1537 0.079 - 0.118: 469 0.118 - 0.158: 143 0.158 - 0.197: 9 Chirality restraints: 6243 Sorted by residual: chirality pdb=" C3' A P 4 " pdb=" C4' A P 4 " pdb=" O3' A P 4 " pdb=" C2' A P 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA PHE A 938 " pdb=" N PHE A 938 " pdb=" C PHE A 938 " pdb=" CB PHE A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" C3' A P 1 " pdb=" C4' A P 1 " pdb=" O3' A P 1 " pdb=" C2' A P 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 6240 not shown) Planarity restraints: 6674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 527 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C ILE I 527 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE I 527 " -0.017 2.00e-02 2.50e+03 pdb=" N SER I 528 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 553 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C THR I 553 " -0.042 2.00e-02 2.50e+03 pdb=" O THR I 553 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP I 554 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.022 2.00e-02 2.50e+03 1.85e-02 5.99e+00 pdb=" CG PHE A 938 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.006 2.00e-02 2.50e+03 ... (remaining 6671 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 280 2.56 - 3.15: 31813 3.15 - 3.73: 61295 3.73 - 4.32: 91223 4.32 - 4.90: 148964 Nonbonded interactions: 333575 Sorted by model distance: nonbonded pdb=" O3' A P 10 " pdb="MG MG A1301 " model vdw 1.978 2.170 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.041 2.170 nonbonded pdb=" OE1 GLU Y 386 " pdb=" OG SER Y 444 " model vdw 2.045 3.040 nonbonded pdb=" O LYS B 60 " pdb=" OG1 THR B 63 " model vdw 2.057 3.040 nonbonded pdb=" OG SER I 388 " pdb=" OD1 ASN I 391 " model vdw 2.095 3.040 ... (remaining 333570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 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: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 44.710 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.005 0.077 40457 Z= 0.266 Angle : 0.677 10.802 54985 Z= 0.401 Chirality : 0.047 0.197 6243 Planarity : 0.004 0.061 6674 Dihedral : 13.769 151.280 15380 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 1.59 % Allowed : 4.60 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4633 helix: 0.33 (0.12), residues: 1788 sheet: -0.76 (0.19), residues: 668 loop : -0.66 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 588 TYR 0.019 0.002 TYR Y 400 PHE 0.042 0.002 PHE A 938 TRP 0.012 0.002 TRP A 365 HIS 0.011 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.27 (40442) covalent geometry : angle 0.67460 / 0.40 (54970) hydrogen bonds : bond 0.14891 / 10.02 ( 1761) hydrogen bonds : angle 5.99777 / 4.17 ( 4927) metal coordination : bond 0.00912 / 0.67 ( 15) metal coordination : angle 3.71138 / 2.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 738 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 140 GLN cc_start: 0.7567 (mp10) cc_final: 0.7108 (pm20) REVERT: A 283 ASP cc_start: 0.8445 (m-30) cc_final: 0.8239 (m-30) REVERT: A 608 LYS cc_start: 0.8548 (tttt) cc_final: 0.8274 (tttm) REVERT: A 1165 GLU cc_start: 0.7791 (tt0) cc_final: 0.7582 (tt0) REVERT: B 9 MET cc_start: 0.8658 (tpt) cc_final: 0.8345 (tpt) REVERT: B 143 ASP cc_start: 0.7719 (t0) cc_final: 0.7485 (p0) REVERT: B 289 ASP cc_start: 0.8154 (m-30) cc_final: 0.7895 (m-30) REVERT: B 310 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 504 ASP cc_start: 0.7833 (t0) cc_final: 0.7597 (t0) REVERT: B 506 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 1151 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8477 (mmtt) REVERT: C 129 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8200 (mm-40) REVERT: C 187 PHE cc_start: 0.9569 (OUTLIER) cc_final: 0.9137 (p90) REVERT: E 117 ASP cc_start: 0.8464 (p0) cc_final: 0.8149 (p0) REVERT: G 125 PHE cc_start: 0.7623 (m-80) cc_final: 0.7134 (m-80) REVERT: I 10 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: I 106 GLU cc_start: 0.7650 (mp0) cc_final: 0.7378 (mp0) REVERT: I 181 GLN cc_start: 0.8833 (tp40) cc_final: 0.8601 (tm-30) REVERT: I 537 LYS cc_start: 0.8942 (tptp) cc_final: 0.8680 (tptp) REVERT: I 550 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8771 (t) REVERT: I 674 HIS cc_start: 0.5913 (m90) cc_final: 0.5472 (m90) REVERT: I 780 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7935 (mt-10) REVERT: I 786 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8361 (mttt) REVERT: S 100 TYR cc_start: 0.8421 (m-80) cc_final: 0.8146 (m-80) REVERT: S 135 ASN cc_start: 0.8942 (t0) cc_final: 0.8722 (t0) REVERT: S 138 LYS cc_start: 0.8866 (mttp) cc_final: 0.8659 (mmtp) REVERT: Y 488 PRO cc_start: 0.8122 (Cg_exo) cc_final: 0.7869 (Cg_endo) outliers start: 68 outliers final: 13 residues processed: 788 average time/residue: 0.7864 time to fit residues: 744.8310 Evaluate side-chains 565 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 549 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain Y residue 246 GLU Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 586 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 412 GLN A 853 ASN A1004 ASN A1199 ASN B 159 ASN B 376 ASN B 481 GLN B 645 GLN E 62 GLN E 89 GLN G 100 GLN G 127 ASN G 133 ASN ** I 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 661 HIS I 664 ASN ** I 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN J 57 GLN Y 176 ASN Y 214 ASN Y 609 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.090514 restraints weight = 56081.225| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.12 r_work: 0.2770 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 40457 Z= 0.214 Angle : 0.632 12.762 54985 Z= 0.337 Chirality : 0.046 0.261 6243 Planarity : 0.004 0.050 6674 Dihedral : 13.670 157.652 5987 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.24 % Allowed : 10.64 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4633 helix: 0.69 (0.12), residues: 1808 sheet: -0.55 (0.19), residues: 674 loop : -0.53 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 328 TYR 0.020 0.002 TYR I 532 PHE 0.033 0.002 PHE A 938 TRP 0.011 0.001 TRP A 131 HIS 0.009 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (40442) covalent geometry : angle 0.62857 / 0.34 (54970) hydrogen bonds : bond 0.05189 / 3.41 ( 1761) hydrogen bonds : angle 4.95508 / 3.43 ( 4927) metal coordination : bond 0.01122 / 0.77 ( 15) metal coordination : angle 4.21586 / 2.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 568 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9070 (mttt) cc_final: 0.8733 (mtpt) REVERT: A 58 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8676 (mt-10) REVERT: A 140 GLN cc_start: 0.7862 (mp10) cc_final: 0.7033 (pm20) REVERT: A 608 LYS cc_start: 0.8618 (tttt) cc_final: 0.8352 (tttm) REVERT: A 1053 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: A 1165 GLU cc_start: 0.8781 (tt0) cc_final: 0.8353 (tt0) REVERT: B 9 MET cc_start: 0.8936 (tpt) cc_final: 0.8661 (tpt) REVERT: B 65 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7091 (ptm-80) REVERT: B 143 ASP cc_start: 0.8462 (t0) cc_final: 0.7810 (p0) REVERT: B 160 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8359 (ptpt) REVERT: B 306 GLU cc_start: 0.8766 (pt0) cc_final: 0.8490 (pt0) REVERT: B 310 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 478 ARG cc_start: 0.7902 (ppt170) cc_final: 0.7184 (ptp90) REVERT: B 504 ASP cc_start: 0.8784 (t0) cc_final: 0.8492 (t0) REVERT: B 506 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 726 LYS cc_start: 0.7282 (tptt) cc_final: 0.6918 (tptt) REVERT: C 15 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: C 129 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8337 (mm-40) REVERT: C 187 PHE cc_start: 0.9609 (OUTLIER) cc_final: 0.9140 (p90) REVERT: E 3 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: E 40 GLU cc_start: 0.8375 (pt0) cc_final: 0.8133 (mt-10) REVERT: E 89 GLN cc_start: 0.9096 (mt0) cc_final: 0.8891 (mt0) REVERT: E 135 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8679 (mttp) REVERT: G 24 LYS cc_start: 0.9063 (mttp) cc_final: 0.8767 (mttp) REVERT: G 117 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: G 121 LYS cc_start: 0.6972 (ttpp) cc_final: 0.6734 (tmmt) REVERT: I 10 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: I 85 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: I 106 GLU cc_start: 0.8310 (mp0) cc_final: 0.7913 (mp0) REVERT: I 181 GLN cc_start: 0.8841 (tp40) cc_final: 0.8463 (tm-30) REVERT: I 205 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8678 (ptpp) REVERT: I 537 LYS cc_start: 0.9321 (tptp) cc_final: 0.8860 (tptp) REVERT: I 550 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8755 (t) REVERT: I 663 THR cc_start: 0.8153 (m) cc_final: 0.7826 (p) REVERT: I 674 HIS cc_start: 0.6449 (m90) cc_final: 0.6094 (m90) REVERT: I 682 LYS cc_start: 0.6826 (mppt) cc_final: 0.6535 (mmtm) REVERT: S 135 ASN cc_start: 0.8677 (t0) cc_final: 0.8333 (t0) REVERT: S 138 LYS cc_start: 0.8658 (mttp) cc_final: 0.8379 (mmtp) REVERT: Y 614 MET cc_start: 0.4479 (tpt) cc_final: 0.4107 (tpt) outliers start: 96 outliers final: 31 residues processed: 621 average time/residue: 0.7908 time to fit residues: 592.1930 Evaluate side-chains 553 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 511 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 541 CYS Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 577 LYS Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 372 CYS Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 586 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 400 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 268 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 853 ASN A1004 ASN B 101 ASN B 481 GLN B 645 GLN C 229 ASN I 178 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 HIS Y 214 ASN ** Y 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 540 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.090864 restraints weight = 56273.948| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.12 r_work: 0.2779 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40457 Z= 0.171 Angle : 0.586 12.756 54985 Z= 0.311 Chirality : 0.045 0.249 6243 Planarity : 0.004 0.047 6674 Dihedral : 13.394 157.755 5975 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.19 % Allowed : 11.66 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4633 helix: 0.89 (0.12), residues: 1805 sheet: -0.41 (0.20), residues: 662 loop : -0.50 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 364 TYR 0.016 0.001 TYR I 492 PHE 0.032 0.002 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.007 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (40442) covalent geometry : angle 0.58205 / 0.31 (54970) hydrogen bonds : bond 0.04620 / 3.01 ( 1761) hydrogen bonds : angle 4.74979 / 3.29 ( 4927) metal coordination : bond 0.00888 / 0.63 ( 15) metal coordination : angle 4.11650 / 2.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 544 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9084 (mttt) cc_final: 0.8742 (mtpt) REVERT: A 58 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 140 GLN cc_start: 0.7898 (mp10) cc_final: 0.7095 (pm20) REVERT: A 149 VAL cc_start: 0.8498 (t) cc_final: 0.8281 (t) REVERT: A 238 GLN cc_start: 0.8203 (tt0) cc_final: 0.7697 (tm-30) REVERT: A 264 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: A 608 LYS cc_start: 0.8649 (tttt) cc_final: 0.8394 (tttm) REVERT: A 1019 ASP cc_start: 0.8461 (m-30) cc_final: 0.8241 (m-30) REVERT: A 1053 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: A 1165 GLU cc_start: 0.8788 (tt0) cc_final: 0.8359 (tt0) REVERT: B 9 MET cc_start: 0.8930 (tpt) cc_final: 0.8666 (tpt) REVERT: B 65 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7223 (ptm-80) REVERT: B 143 ASP cc_start: 0.8448 (t0) cc_final: 0.7818 (p0) REVERT: B 160 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8149 (ptpt) REVERT: B 306 GLU cc_start: 0.8767 (pt0) cc_final: 0.8501 (pt0) REVERT: B 310 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 478 ARG cc_start: 0.7928 (ppt170) cc_final: 0.7202 (ptp90) REVERT: B 504 ASP cc_start: 0.8795 (t0) cc_final: 0.8502 (t0) REVERT: B 506 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 726 LYS cc_start: 0.7334 (tptt) cc_final: 0.7096 (tptt) REVERT: B 1047 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7856 (mtm180) REVERT: C 15 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8298 (tp30) REVERT: C 129 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8294 (mm-40) REVERT: C 152 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: C 187 PHE cc_start: 0.9601 (OUTLIER) cc_final: 0.9074 (p90) REVERT: E 3 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: E 40 GLU cc_start: 0.8366 (pt0) cc_final: 0.8105 (mt-10) REVERT: E 135 LYS cc_start: 0.8907 (mptp) cc_final: 0.8644 (mttp) REVERT: G 24 LYS cc_start: 0.9037 (mttp) cc_final: 0.8836 (mttp) REVERT: G 92 GLU cc_start: 0.7903 (pm20) cc_final: 0.7619 (pm20) REVERT: G 100 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: G 117 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: G 121 LYS cc_start: 0.6941 (ttpp) cc_final: 0.6693 (tmmt) REVERT: I 10 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: I 85 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: I 106 GLU cc_start: 0.8303 (mp0) cc_final: 0.7898 (mp0) REVERT: I 181 GLN cc_start: 0.8863 (tp40) cc_final: 0.8438 (tm-30) REVERT: I 300 LYS cc_start: 0.8267 (tppp) cc_final: 0.8050 (tppt) REVERT: I 421 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7803 (mmt) REVERT: I 487 MET cc_start: 0.7940 (tpt) cc_final: 0.7702 (tpp) REVERT: I 537 LYS cc_start: 0.9331 (tptp) cc_final: 0.8962 (tptp) REVERT: I 663 THR cc_start: 0.8126 (m) cc_final: 0.7887 (p) REVERT: I 674 HIS cc_start: 0.6445 (m90) cc_final: 0.6121 (m90) REVERT: I 682 LYS cc_start: 0.6803 (mppt) cc_final: 0.6534 (mmtm) REVERT: I 719 GLU cc_start: 0.6948 (tp30) cc_final: 0.6741 (tp30) REVERT: I 758 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: S 135 ASN cc_start: 0.8685 (t0) cc_final: 0.8333 (t0) REVERT: S 138 LYS cc_start: 0.8650 (mttp) cc_final: 0.8359 (mmtp) REVERT: Y 614 MET cc_start: 0.4713 (tpt) cc_final: 0.4348 (tpt) outliers start: 94 outliers final: 30 residues processed: 601 average time/residue: 0.8112 time to fit residues: 585.7789 Evaluate side-chains 571 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 164 VAL Chi-restraints excluded: chain Y residue 372 CYS Chi-restraints excluded: chain Y residue 525 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 457 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 124 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN A 230 ASN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN B 481 GLN B 496 ASN B 645 GLN B 754 GLN C 229 ASN E 89 GLN I 178 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Y 214 ASN Y 272 GLN ** Y 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091874 restraints weight = 56000.514| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.19 r_work: 0.2787 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40457 Z= 0.137 Angle : 0.562 11.708 54985 Z= 0.296 Chirality : 0.044 0.256 6243 Planarity : 0.004 0.045 6674 Dihedral : 13.283 158.293 5971 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.10 % Allowed : 12.27 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4633 helix: 1.05 (0.12), residues: 1818 sheet: -0.34 (0.20), residues: 660 loop : -0.43 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 110 TYR 0.025 0.001 TYR I 532 PHE 0.030 0.001 PHE A 938 TRP 0.012 0.001 TRP Y 94 HIS 0.007 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (40442) covalent geometry : angle 0.55807 / 0.30 (54970) hydrogen bonds : bond 0.04128 / 2.68 ( 1761) hydrogen bonds : angle 4.60164 / 3.19 ( 4927) metal coordination : bond 0.00693 / 0.51 ( 15) metal coordination : angle 3.86535 / 2.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 553 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9062 (mttt) cc_final: 0.8739 (mtpt) REVERT: A 58 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8672 (mt-10) REVERT: A 140 GLN cc_start: 0.7947 (mp10) cc_final: 0.7107 (pm20) REVERT: A 149 VAL cc_start: 0.8489 (t) cc_final: 0.8225 (t) REVERT: A 238 GLN cc_start: 0.8211 (tt0) cc_final: 0.7679 (tm-30) REVERT: A 251 LYS cc_start: 0.9073 (mttm) cc_final: 0.8766 (mmtm) REVERT: A 1019 ASP cc_start: 0.8470 (m-30) cc_final: 0.8255 (m-30) REVERT: A 1079 GLU cc_start: 0.7795 (mp0) cc_final: 0.7573 (pm20) REVERT: A 1165 GLU cc_start: 0.8794 (tt0) cc_final: 0.8370 (tt0) REVERT: B 9 MET cc_start: 0.8921 (tpt) cc_final: 0.8636 (tpt) REVERT: B 143 ASP cc_start: 0.8458 (t0) cc_final: 0.7813 (p0) REVERT: B 160 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8167 (ptpt) REVERT: B 255 ASP cc_start: 0.8548 (t0) cc_final: 0.8225 (t0) REVERT: B 302 LEU cc_start: 0.8972 (mt) cc_final: 0.8431 (mt) REVERT: B 306 GLU cc_start: 0.8776 (pt0) cc_final: 0.7899 (pp20) REVERT: B 310 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 478 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7117 (ptp90) REVERT: B 506 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 781 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: B 1098 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: C 15 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: C 152 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: C 187 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.9031 (p90) REVERT: E 40 GLU cc_start: 0.8372 (pt0) cc_final: 0.8093 (mt-10) REVERT: E 135 LYS cc_start: 0.8835 (mptp) cc_final: 0.8541 (mttp) REVERT: G 73 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9018 (m) REVERT: G 92 GLU cc_start: 0.7875 (pm20) cc_final: 0.7603 (pm20) REVERT: G 100 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: G 117 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: G 121 LYS cc_start: 0.6965 (ttpp) cc_final: 0.6697 (tmmt) REVERT: G 159 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7540 (m) REVERT: I 106 GLU cc_start: 0.8324 (mp0) cc_final: 0.7923 (mp0) REVERT: I 181 GLN cc_start: 0.8890 (tp40) cc_final: 0.8426 (tm-30) REVERT: I 421 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7796 (mmt) REVERT: I 487 MET cc_start: 0.7907 (tpt) cc_final: 0.7675 (tpp) REVERT: I 537 LYS cc_start: 0.9303 (tptp) cc_final: 0.8739 (tptp) REVERT: I 674 HIS cc_start: 0.6466 (m90) cc_final: 0.6063 (m90) REVERT: I 682 LYS cc_start: 0.6758 (mppt) cc_final: 0.6520 (mmtm) REVERT: I 719 GLU cc_start: 0.7001 (tp30) cc_final: 0.6729 (tp30) REVERT: I 758 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: J 36 LYS cc_start: 0.9206 (tttm) cc_final: 0.8963 (tttt) REVERT: S 135 ASN cc_start: 0.8698 (t0) cc_final: 0.8326 (t0) REVERT: S 138 LYS cc_start: 0.8634 (mttp) cc_final: 0.8328 (mmtp) REVERT: Y 614 MET cc_start: 0.4805 (tpt) cc_final: 0.4468 (tpt) outliers start: 90 outliers final: 30 residues processed: 601 average time/residue: 0.8266 time to fit residues: 596.4117 Evaluate side-chains 557 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 514 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1098 LYS Chi-restraints excluded: chain B residue 1151 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 394 optimal weight: 50.0000 chunk 321 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 chunk 466 optimal weight: 50.0000 chunk 467 optimal weight: 50.0000 chunk 299 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 296 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN A1004 ASN B 376 ASN B 481 GLN B 645 GLN C 229 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091823 restraints weight = 56066.907| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.11 r_work: 0.2802 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40457 Z= 0.146 Angle : 0.563 12.096 54985 Z= 0.297 Chirality : 0.044 0.262 6243 Planarity : 0.004 0.044 6674 Dihedral : 13.240 158.507 5967 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 12.78 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4633 helix: 1.12 (0.12), residues: 1817 sheet: -0.30 (0.20), residues: 648 loop : -0.41 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 86 TYR 0.016 0.001 TYR I 492 PHE 0.031 0.001 PHE A 938 TRP 0.011 0.001 TRP Y 94 HIS 0.007 0.001 HIS Y 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (40442) covalent geometry : angle 0.55944 / 0.30 (54970) hydrogen bonds : bond 0.04104 / 2.67 ( 1761) hydrogen bonds : angle 4.55984 / 3.16 ( 4927) metal coordination : bond 0.00722 / 0.52 ( 15) metal coordination : angle 3.81564 / 2.09 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 539 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9052 (mttt) cc_final: 0.8729 (mtpt) REVERT: A 58 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 140 GLN cc_start: 0.7955 (mp10) cc_final: 0.7113 (pm20) REVERT: A 149 VAL cc_start: 0.8510 (t) cc_final: 0.8264 (t) REVERT: A 238 GLN cc_start: 0.8210 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 251 LYS cc_start: 0.9115 (mttm) cc_final: 0.8838 (mmtm) REVERT: A 1019 ASP cc_start: 0.8455 (m-30) cc_final: 0.8227 (m-30) REVERT: A 1042 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: A 1165 GLU cc_start: 0.8797 (tt0) cc_final: 0.8407 (tt0) REVERT: B 9 MET cc_start: 0.8935 (tpt) cc_final: 0.8632 (tpt) REVERT: B 65 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7137 (ptm-80) REVERT: B 143 ASP cc_start: 0.8426 (t0) cc_final: 0.7777 (p0) REVERT: B 160 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8186 (ptpt) REVERT: B 255 ASP cc_start: 0.8537 (t0) cc_final: 0.8215 (t0) REVERT: B 306 GLU cc_start: 0.8754 (pt0) cc_final: 0.8477 (pt0) REVERT: B 310 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 478 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7586 (ppt170) REVERT: B 506 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 781 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: B 983 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: B 1047 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7848 (mtm180) REVERT: B 1098 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (mtpt) REVERT: C 15 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: C 129 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8413 (mm-40) REVERT: C 152 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: C 187 PHE cc_start: 0.9590 (OUTLIER) cc_final: 0.9022 (p90) REVERT: E 3 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: E 40 GLU cc_start: 0.8352 (pt0) cc_final: 0.8072 (mt-10) REVERT: E 80 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: E 135 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8555 (mttp) REVERT: G 38 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8311 (ttm110) REVERT: G 92 GLU cc_start: 0.7840 (pm20) cc_final: 0.7536 (pm20) REVERT: G 100 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8510 (mp10) REVERT: G 117 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: G 121 LYS cc_start: 0.7025 (ttpp) cc_final: 0.6746 (tmmt) REVERT: G 159 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7576 (m) REVERT: I 106 GLU cc_start: 0.8305 (mp0) cc_final: 0.7907 (mp0) REVERT: I 181 GLN cc_start: 0.8909 (tp40) cc_final: 0.8440 (tm-30) REVERT: I 238 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: I 300 LYS cc_start: 0.8235 (tppp) cc_final: 0.8024 (tppt) REVERT: I 317 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7969 (mtp180) REVERT: I 421 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7813 (mmt) REVERT: I 487 MET cc_start: 0.7919 (tpt) cc_final: 0.7687 (tpp) REVERT: I 537 LYS cc_start: 0.9282 (tptp) cc_final: 0.8760 (tptp) REVERT: I 674 HIS cc_start: 0.6486 (m90) cc_final: 0.6198 (m90) REVERT: I 682 LYS cc_start: 0.6730 (mppt) cc_final: 0.6508 (mmtm) REVERT: I 719 GLU cc_start: 0.6943 (tp30) cc_final: 0.6640 (tp30) REVERT: I 758 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: J 36 LYS cc_start: 0.9199 (tttm) cc_final: 0.8959 (tttt) REVERT: S 135 ASN cc_start: 0.8716 (t0) cc_final: 0.8345 (t0) REVERT: S 138 LYS cc_start: 0.8614 (mttp) cc_final: 0.8317 (mmtp) REVERT: Y 463 MET cc_start: 0.7423 (tpp) cc_final: 0.7211 (mmt) REVERT: Y 614 MET cc_start: 0.4858 (tpt) cc_final: 0.4516 (tpt) outliers start: 91 outliers final: 37 residues processed: 586 average time/residue: 0.8096 time to fit residues: 570.3682 Evaluate side-chains 576 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 520 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain B residue 1098 LYS Chi-restraints excluded: chain B residue 1151 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 295 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 164 optimal weight: 40.0000 chunk 193 optimal weight: 2.9990 chunk 413 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 315 optimal weight: 40.0000 chunk 127 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A1004 ASN B 101 ASN B 376 ASN B 481 GLN B 645 GLN B 754 GLN C 229 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.090228 restraints weight = 56580.187| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.13 r_work: 0.2790 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40457 Z= 0.189 Angle : 0.581 13.207 54985 Z= 0.307 Chirality : 0.045 0.265 6243 Planarity : 0.004 0.043 6674 Dihedral : 13.247 158.829 5965 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 13.13 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 4633 helix: 1.10 (0.12), residues: 1818 sheet: -0.23 (0.20), residues: 643 loop : -0.41 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 51 TYR 0.022 0.001 TYR B 15 PHE 0.032 0.002 PHE A 938 TRP 0.011 0.001 TRP Y 94 HIS 0.008 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (40442) covalent geometry : angle 0.57722 / 0.31 (54970) hydrogen bonds : bond 0.04311 / 2.82 ( 1761) hydrogen bonds : angle 4.56508 / 3.17 ( 4927) metal coordination : bond 0.00897 / 0.64 ( 15) metal coordination : angle 4.00371 / 2.17 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 537 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9071 (mttt) cc_final: 0.8747 (mtpt) REVERT: A 58 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 140 GLN cc_start: 0.7951 (mp10) cc_final: 0.7157 (pm20) REVERT: A 149 VAL cc_start: 0.8535 (t) cc_final: 0.8223 (t) REVERT: A 238 GLN cc_start: 0.8152 (tt0) cc_final: 0.7593 (tm-30) REVERT: A 251 LYS cc_start: 0.9127 (mttm) cc_final: 0.8850 (mmtm) REVERT: A 1019 ASP cc_start: 0.8471 (m-30) cc_final: 0.8243 (m-30) REVERT: A 1042 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 1165 GLU cc_start: 0.8830 (tt0) cc_final: 0.8449 (tt0) REVERT: B 9 MET cc_start: 0.8970 (tpt) cc_final: 0.8675 (tpt) REVERT: B 65 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7174 (ptm-80) REVERT: B 143 ASP cc_start: 0.8460 (t0) cc_final: 0.7783 (p0) REVERT: B 160 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8310 (ptpt) REVERT: B 255 ASP cc_start: 0.8567 (t0) cc_final: 0.8260 (t0) REVERT: B 289 ASP cc_start: 0.8578 (m-30) cc_final: 0.8254 (m-30) REVERT: B 302 LEU cc_start: 0.8957 (mt) cc_final: 0.8279 (mt) REVERT: B 306 GLU cc_start: 0.8786 (pt0) cc_final: 0.7944 (pp20) REVERT: B 310 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 506 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 781 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: B 983 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: B 1047 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7857 (mtm180) REVERT: B 1098 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: C 15 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: C 129 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8356 (mm-40) REVERT: C 152 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: C 187 PHE cc_start: 0.9603 (OUTLIER) cc_final: 0.9083 (p90) REVERT: E 3 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: E 40 GLU cc_start: 0.8367 (pt0) cc_final: 0.8091 (mt-10) REVERT: E 80 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: E 135 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: G 38 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8300 (ttm110) REVERT: G 92 GLU cc_start: 0.7847 (pm20) cc_final: 0.7504 (pm20) REVERT: G 100 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: G 117 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: G 121 LYS cc_start: 0.7049 (ttpp) cc_final: 0.6754 (tmmt) REVERT: G 159 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7595 (m) REVERT: I 106 GLU cc_start: 0.8300 (mp0) cc_final: 0.7909 (mp0) REVERT: I 181 GLN cc_start: 0.8926 (tp40) cc_final: 0.8322 (tm-30) REVERT: I 238 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: I 317 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7984 (mtp180) REVERT: I 421 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7857 (mmt) REVERT: I 487 MET cc_start: 0.7920 (tpt) cc_final: 0.7686 (tpp) REVERT: I 537 LYS cc_start: 0.9275 (tptp) cc_final: 0.8816 (tptp) REVERT: I 643 LYS cc_start: 0.9213 (mtpm) cc_final: 0.8893 (mttp) REVERT: I 674 HIS cc_start: 0.6487 (m90) cc_final: 0.5492 (m90) REVERT: I 682 LYS cc_start: 0.6747 (mppt) cc_final: 0.6513 (mmtm) REVERT: I 719 GLU cc_start: 0.7079 (tp30) cc_final: 0.6746 (tp30) REVERT: I 757 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8165 (ptp-110) REVERT: I 758 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: J 36 LYS cc_start: 0.9217 (tttm) cc_final: 0.8983 (tttt) REVERT: Y 217 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8970 (tt) REVERT: Y 263 MET cc_start: 0.5735 (ppp) cc_final: 0.5271 (ppp) REVERT: Y 463 MET cc_start: 0.7600 (tpp) cc_final: 0.7369 (mmt) REVERT: Y 614 MET cc_start: 0.4885 (tpt) cc_final: 0.4546 (tpt) outliers start: 92 outliers final: 38 residues processed: 588 average time/residue: 0.8267 time to fit residues: 583.1650 Evaluate side-chains 580 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 521 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain B residue 1098 LYS Chi-restraints excluded: chain B residue 1151 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 757 ARG Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 31 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 422 optimal weight: 0.6980 chunk 356 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN B 481 GLN B 645 GLN C 229 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091677 restraints weight = 56218.655| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.10 r_work: 0.2812 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40457 Z= 0.135 Angle : 0.560 12.744 54985 Z= 0.295 Chirality : 0.044 0.265 6243 Planarity : 0.004 0.063 6674 Dihedral : 13.209 158.943 5965 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.89 % Allowed : 13.83 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.12), residues: 4633 helix: 1.20 (0.12), residues: 1816 sheet: -0.18 (0.20), residues: 635 loop : -0.37 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 86 TYR 0.030 0.001 TYR I 532 PHE 0.029 0.001 PHE A 938 TRP 0.011 0.001 TRP A 365 HIS 0.010 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (40442) covalent geometry : angle 0.55674 / 0.30 (54970) hydrogen bonds : bond 0.03954 / 2.57 ( 1761) hydrogen bonds : angle 4.50890 / 3.13 ( 4927) metal coordination : bond 0.00642 / 0.47 ( 15) metal coordination : angle 3.73210 / 2.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 552 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9055 (mttt) cc_final: 0.8753 (mtpt) REVERT: A 58 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8624 (mt-10) REVERT: A 140 GLN cc_start: 0.7966 (mp10) cc_final: 0.6967 (pm20) REVERT: A 238 GLN cc_start: 0.8220 (tt0) cc_final: 0.7730 (tm-30) REVERT: A 251 LYS cc_start: 0.9121 (mttm) cc_final: 0.8919 (mmtm) REVERT: A 1019 ASP cc_start: 0.8458 (m-30) cc_final: 0.8229 (m-30) REVERT: A 1165 GLU cc_start: 0.8810 (tt0) cc_final: 0.8419 (tt0) REVERT: B 9 MET cc_start: 0.8947 (tpt) cc_final: 0.8643 (tpt) REVERT: B 65 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7109 (ptm-80) REVERT: B 143 ASP cc_start: 0.8421 (t0) cc_final: 0.7761 (p0) REVERT: B 160 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8133 (ptpt) REVERT: B 255 ASP cc_start: 0.8537 (t0) cc_final: 0.8245 (t0) REVERT: B 289 ASP cc_start: 0.8585 (m-30) cc_final: 0.8281 (m-30) REVERT: B 302 LEU cc_start: 0.8927 (mt) cc_final: 0.8413 (mt) REVERT: B 306 GLU cc_start: 0.8779 (pt0) cc_final: 0.7910 (pp20) REVERT: B 310 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 506 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 781 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: B 804 ASN cc_start: 0.8651 (t160) cc_final: 0.8362 (t160) REVERT: B 983 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 1047 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7789 (mtm180) REVERT: C 15 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: C 129 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8381 (mm-40) REVERT: C 152 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: C 187 PHE cc_start: 0.9575 (OUTLIER) cc_final: 0.8962 (p90) REVERT: E 3 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: E 40 GLU cc_start: 0.8362 (pt0) cc_final: 0.8082 (mt-10) REVERT: E 80 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: E 135 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: G 92 GLU cc_start: 0.7817 (pm20) cc_final: 0.7489 (pm20) REVERT: G 96 ASN cc_start: 0.9144 (m-40) cc_final: 0.8795 (m110) REVERT: G 117 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: G 121 LYS cc_start: 0.7028 (ttpp) cc_final: 0.6724 (tmmt) REVERT: G 159 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7658 (m) REVERT: I 88 VAL cc_start: 0.6204 (OUTLIER) cc_final: 0.5970 (m) REVERT: I 106 GLU cc_start: 0.8303 (mp0) cc_final: 0.7899 (mp0) REVERT: I 181 GLN cc_start: 0.8919 (tp40) cc_final: 0.8299 (tm-30) REVERT: I 238 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: I 253 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8613 (p0) REVERT: I 317 ARG cc_start: 0.8320 (mtp180) cc_final: 0.7970 (mtp180) REVERT: I 421 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7853 (mmt) REVERT: I 487 MET cc_start: 0.7942 (tpt) cc_final: 0.7722 (tpp) REVERT: I 537 LYS cc_start: 0.9260 (tptp) cc_final: 0.8688 (tptp) REVERT: I 643 LYS cc_start: 0.9208 (mtpm) cc_final: 0.8907 (mttp) REVERT: I 682 LYS cc_start: 0.6738 (mppt) cc_final: 0.6514 (mmtm) REVERT: I 719 GLU cc_start: 0.6982 (tp30) cc_final: 0.6648 (tp30) REVERT: I 758 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: J 36 LYS cc_start: 0.9210 (tttm) cc_final: 0.8973 (tttt) REVERT: S 135 ASN cc_start: 0.8486 (t0) cc_final: 0.8124 (t0) REVERT: Y 263 MET cc_start: 0.5615 (ppp) cc_final: 0.5235 (ppp) REVERT: Y 463 MET cc_start: 0.7745 (tpp) cc_final: 0.7480 (mmt) REVERT: Y 614 MET cc_start: 0.4926 (tpt) cc_final: 0.4702 (tpt) outliers start: 81 outliers final: 34 residues processed: 604 average time/residue: 0.8111 time to fit residues: 590.4099 Evaluate side-chains 583 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 531 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 428 GLN Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 187 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 393 optimal weight: 60.0000 chunk 355 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 645 GLN C 229 ASN G 100 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.090466 restraints weight = 56231.987| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.13 r_work: 0.2795 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40457 Z= 0.180 Angle : 0.585 13.793 54985 Z= 0.307 Chirality : 0.045 0.262 6243 Planarity : 0.004 0.043 6674 Dihedral : 13.233 159.457 5965 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.87 % Allowed : 14.37 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4633 helix: 1.14 (0.12), residues: 1825 sheet: -0.19 (0.20), residues: 635 loop : -0.39 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 86 TYR 0.022 0.001 TYR I 532 PHE 0.032 0.001 PHE A 938 TRP 0.009 0.001 TRP Y 94 HIS 0.014 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (40442) covalent geometry : angle 0.58104 / 0.31 (54970) hydrogen bonds : bond 0.04195 / 2.74 ( 1761) hydrogen bonds : angle 4.52378 / 3.14 ( 4927) metal coordination : bond 0.00831 / 0.60 ( 15) metal coordination : angle 3.90859 / 2.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 532 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9078 (mttt) cc_final: 0.8847 (mtpt) REVERT: A 58 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 140 GLN cc_start: 0.8119 (mp10) cc_final: 0.7193 (pm20) REVERT: A 141 LYS cc_start: 0.8304 (tppt) cc_final: 0.7912 (tmmt) REVERT: A 149 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 238 GLN cc_start: 0.8248 (tt0) cc_final: 0.7717 (tm-30) REVERT: A 251 LYS cc_start: 0.9118 (mttm) cc_final: 0.8843 (mmtm) REVERT: A 1019 ASP cc_start: 0.8474 (m-30) cc_final: 0.8261 (m-30) REVERT: A 1165 GLU cc_start: 0.8838 (tt0) cc_final: 0.8451 (tt0) REVERT: B 9 MET cc_start: 0.8967 (tpt) cc_final: 0.8682 (tpt) REVERT: B 65 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7137 (ptm-80) REVERT: B 143 ASP cc_start: 0.8432 (t0) cc_final: 0.7811 (p0) REVERT: B 160 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8135 (ptpt) REVERT: B 302 LEU cc_start: 0.8964 (mt) cc_final: 0.8483 (mt) REVERT: B 306 GLU cc_start: 0.8785 (pt0) cc_final: 0.7915 (pp20) REVERT: B 310 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 504 ASP cc_start: 0.8791 (t0) cc_final: 0.8484 (t0) REVERT: B 506 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 804 ASN cc_start: 0.8664 (t160) cc_final: 0.8381 (t160) REVERT: B 983 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: B 1047 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7825 (mtm180) REVERT: C 15 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: C 129 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8391 (mm-40) REVERT: C 152 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: C 187 PHE cc_start: 0.9598 (OUTLIER) cc_final: 0.9051 (p90) REVERT: E 3 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: E 40 GLU cc_start: 0.8370 (pt0) cc_final: 0.8095 (mt-10) REVERT: E 80 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: E 135 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8655 (mttp) REVERT: G 38 ARG cc_start: 0.8882 (ttm110) cc_final: 0.8297 (ttm110) REVERT: G 92 GLU cc_start: 0.7850 (pm20) cc_final: 0.7512 (pm20) REVERT: G 96 ASN cc_start: 0.9141 (m-40) cc_final: 0.8743 (m110) REVERT: G 117 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: G 121 LYS cc_start: 0.7043 (ttpp) cc_final: 0.6713 (tmmt) REVERT: G 159 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7688 (m) REVERT: I 88 VAL cc_start: 0.6167 (OUTLIER) cc_final: 0.5942 (m) REVERT: I 106 GLU cc_start: 0.8309 (mp0) cc_final: 0.7905 (mp0) REVERT: I 181 GLN cc_start: 0.8902 (tp40) cc_final: 0.8589 (tp40) REVERT: I 238 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: I 253 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8606 (p0) REVERT: I 317 ARG cc_start: 0.8310 (mtp180) cc_final: 0.7960 (mtp180) REVERT: I 421 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7882 (mmt) REVERT: I 487 MET cc_start: 0.7956 (tpt) cc_final: 0.7730 (tpp) REVERT: I 537 LYS cc_start: 0.9234 (tptp) cc_final: 0.8687 (tptp) REVERT: I 643 LYS cc_start: 0.9208 (mtpm) cc_final: 0.8905 (mttp) REVERT: I 682 LYS cc_start: 0.6770 (mppt) cc_final: 0.6511 (mmtm) REVERT: I 719 GLU cc_start: 0.7130 (tp30) cc_final: 0.6820 (tp30) REVERT: I 758 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: J 36 LYS cc_start: 0.9220 (tttm) cc_final: 0.8984 (tttt) REVERT: S 135 ASN cc_start: 0.8534 (t0) cc_final: 0.8172 (t0) REVERT: Y 263 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.5287 (ppp) REVERT: Y 463 MET cc_start: 0.7742 (tpp) cc_final: 0.7447 (mmt) REVERT: Y 614 MET cc_start: 0.4915 (tpt) cc_final: 0.4599 (tpt) outliers start: 80 outliers final: 36 residues processed: 579 average time/residue: 0.8294 time to fit residues: 576.5138 Evaluate side-chains 574 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 519 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain B residue 1151 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 758 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 263 MET Chi-restraints excluded: chain Y residue 428 GLN Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 310 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 440 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN B 101 ASN B 481 GLN B 645 GLN C 229 ASN G 100 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Y 189 ASN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 214 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.090516 restraints weight = 56299.696| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.13 r_work: 0.2788 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40457 Z= 0.181 Angle : 0.601 14.974 54985 Z= 0.314 Chirality : 0.045 0.254 6243 Planarity : 0.004 0.050 6674 Dihedral : 13.252 159.700 5965 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.82 % Allowed : 14.63 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4633 helix: 1.12 (0.12), residues: 1824 sheet: -0.19 (0.20), residues: 640 loop : -0.39 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 466 TYR 0.022 0.001 TYR I 532 PHE 0.032 0.001 PHE A 938 TRP 0.009 0.001 TRP Y 94 HIS 0.013 0.001 HIS I 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (40442) covalent geometry : angle 0.59725 / 0.31 (54970) hydrogen bonds : bond 0.04214 / 2.76 ( 1761) hydrogen bonds : angle 4.54191 / 3.15 ( 4927) metal coordination : bond 0.00830 / 0.60 ( 15) metal coordination : angle 3.95336 / 2.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 525 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9075 (mttt) cc_final: 0.8796 (mtpt) REVERT: A 58 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 140 GLN cc_start: 0.8143 (mp10) cc_final: 0.7210 (pm20) REVERT: A 141 LYS cc_start: 0.8329 (tppt) cc_final: 0.7860 (tmmt) REVERT: A 149 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 181 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 230 ASN cc_start: 0.9087 (m-40) cc_final: 0.8878 (m110) REVERT: A 238 GLN cc_start: 0.8157 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 251 LYS cc_start: 0.9115 (mttm) cc_final: 0.8838 (mmtm) REVERT: A 1019 ASP cc_start: 0.8469 (m-30) cc_final: 0.8259 (m-30) REVERT: A 1042 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: A 1165 GLU cc_start: 0.8841 (tt0) cc_final: 0.8454 (tt0) REVERT: B 9 MET cc_start: 0.8981 (tpt) cc_final: 0.8696 (tpt) REVERT: B 59 PHE cc_start: 0.7732 (m-80) cc_final: 0.7281 (m-80) REVERT: B 65 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7148 (ptm-80) REVERT: B 143 ASP cc_start: 0.8420 (t0) cc_final: 0.7809 (p0) REVERT: B 160 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8153 (ptpt) REVERT: B 255 ASP cc_start: 0.8569 (t0) cc_final: 0.8264 (t0) REVERT: B 289 ASP cc_start: 0.8575 (m-30) cc_final: 0.8251 (m-30) REVERT: B 302 LEU cc_start: 0.8996 (mt) cc_final: 0.8492 (mt) REVERT: B 306 GLU cc_start: 0.8782 (pt0) cc_final: 0.7901 (pp20) REVERT: B 310 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 478 ARG cc_start: 0.6831 (ppt170) cc_final: 0.6584 (ppt170) REVERT: B 504 ASP cc_start: 0.8796 (t0) cc_final: 0.8489 (t0) REVERT: B 506 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 804 ASN cc_start: 0.8673 (t160) cc_final: 0.8384 (t160) REVERT: B 983 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: B 1047 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7838 (mtm180) REVERT: C 15 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: C 129 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8451 (mm-40) REVERT: C 152 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: C 187 PHE cc_start: 0.9593 (OUTLIER) cc_final: 0.9026 (p90) REVERT: E 3 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: E 40 GLU cc_start: 0.8358 (pt0) cc_final: 0.8093 (mt-10) REVERT: E 80 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: E 135 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8627 (mttp) REVERT: G 92 GLU cc_start: 0.7850 (pm20) cc_final: 0.7509 (pm20) REVERT: G 96 ASN cc_start: 0.9150 (m-40) cc_final: 0.8738 (m110) REVERT: G 117 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: G 121 LYS cc_start: 0.7062 (ttpp) cc_final: 0.6718 (tmmt) REVERT: G 159 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7719 (m) REVERT: I 85 GLU cc_start: 0.7673 (pt0) cc_final: 0.7221 (pm20) REVERT: I 88 VAL cc_start: 0.6202 (OUTLIER) cc_final: 0.5966 (m) REVERT: I 106 GLU cc_start: 0.8312 (mp0) cc_final: 0.7906 (mp0) REVERT: I 181 GLN cc_start: 0.8919 (tp40) cc_final: 0.8598 (tp40) REVERT: I 238 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: I 317 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7973 (mtp180) REVERT: I 421 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7890 (mmt) REVERT: I 487 MET cc_start: 0.7971 (tpt) cc_final: 0.7748 (tpp) REVERT: I 537 LYS cc_start: 0.9229 (tptp) cc_final: 0.8701 (tptp) REVERT: I 643 LYS cc_start: 0.9213 (mtpm) cc_final: 0.8921 (mttp) REVERT: I 682 LYS cc_start: 0.6735 (mppt) cc_final: 0.6439 (mmtm) REVERT: I 719 GLU cc_start: 0.7062 (tp30) cc_final: 0.6723 (tp30) REVERT: J 36 LYS cc_start: 0.9230 (tttm) cc_final: 0.8992 (tttt) REVERT: S 84 ASN cc_start: 0.8944 (m-40) cc_final: 0.8640 (m110) REVERT: S 135 ASN cc_start: 0.8563 (t0) cc_final: 0.8224 (t0) REVERT: Y 263 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5294 (ppp) REVERT: Y 463 MET cc_start: 0.7808 (tpp) cc_final: 0.7561 (mmt) REVERT: Y 614 MET cc_start: 0.4952 (tpt) cc_final: 0.4624 (tpt) outliers start: 78 outliers final: 39 residues processed: 573 average time/residue: 0.8205 time to fit residues: 565.2775 Evaluate side-chains 572 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 515 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 263 MET Chi-restraints excluded: chain Y residue 525 VAL Chi-restraints excluded: chain Y residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 345 optimal weight: 40.0000 chunk 279 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 404 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN B 481 GLN B 645 GLN C 229 ASN G 100 GLN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Y 207 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.090145 restraints weight = 56019.669| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.12 r_work: 0.2781 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 40457 Z= 0.191 Angle : 0.611 13.495 54985 Z= 0.319 Chirality : 0.045 0.236 6243 Planarity : 0.004 0.050 6674 Dihedral : 13.268 159.947 5965 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.49 % Allowed : 15.19 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 4633 helix: 1.11 (0.12), residues: 1824 sheet: -0.17 (0.20), residues: 638 loop : -0.41 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 466 TYR 0.021 0.001 TYR I 532 PHE 0.032 0.002 PHE A 938 TRP 0.010 0.001 TRP Y 94 HIS 0.008 0.001 HIS Y 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (40442) covalent geometry : angle 0.60735 / 0.32 (54970) hydrogen bonds : bond 0.04272 / 2.80 ( 1761) hydrogen bonds : angle 4.56013 / 3.17 ( 4927) metal coordination : bond 0.00855 / 0.63 ( 15) metal coordination : angle 3.99291 / 2.16 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 527 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9094 (mttt) cc_final: 0.8851 (mtpt) REVERT: A 58 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8638 (mt-10) REVERT: A 140 GLN cc_start: 0.8160 (mp10) cc_final: 0.7236 (pm20) REVERT: A 141 LYS cc_start: 0.8325 (tppt) cc_final: 0.7880 (tmmt) REVERT: A 149 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8267 (t) REVERT: A 181 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 238 GLN cc_start: 0.8210 (tt0) cc_final: 0.7727 (tm-30) REVERT: A 251 LYS cc_start: 0.9113 (mttm) cc_final: 0.8835 (mmtm) REVERT: A 1019 ASP cc_start: 0.8475 (m-30) cc_final: 0.8263 (m-30) REVERT: A 1042 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: A 1165 GLU cc_start: 0.8843 (tt0) cc_final: 0.8419 (tt0) REVERT: B 9 MET cc_start: 0.8981 (tpt) cc_final: 0.8705 (tpt) REVERT: B 59 PHE cc_start: 0.7765 (m-80) cc_final: 0.7304 (m-80) REVERT: B 65 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7130 (ptm-80) REVERT: B 160 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8215 (ptpt) REVERT: B 302 LEU cc_start: 0.9005 (mt) cc_final: 0.8487 (mt) REVERT: B 306 GLU cc_start: 0.8789 (pt0) cc_final: 0.7910 (pp20) REVERT: B 310 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 389 HIS cc_start: 0.7134 (t-170) cc_final: 0.6805 (t70) REVERT: B 478 ARG cc_start: 0.6846 (ppt170) cc_final: 0.6640 (ppt170) REVERT: B 504 ASP cc_start: 0.8805 (t0) cc_final: 0.8499 (t0) REVERT: B 506 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 804 ASN cc_start: 0.8687 (t160) cc_final: 0.8388 (t160) REVERT: B 983 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 1047 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7806 (mtm180) REVERT: C 15 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: C 129 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8401 (mm-40) REVERT: C 152 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: C 187 PHE cc_start: 0.9596 (OUTLIER) cc_final: 0.9110 (p90) REVERT: E 3 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8737 (pt0) REVERT: E 40 GLU cc_start: 0.8366 (pt0) cc_final: 0.8103 (mt-10) REVERT: E 80 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: E 135 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8649 (mttp) REVERT: G 92 GLU cc_start: 0.7871 (pm20) cc_final: 0.7500 (pm20) REVERT: G 96 ASN cc_start: 0.9158 (m-40) cc_final: 0.8701 (m110) REVERT: G 117 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: G 121 LYS cc_start: 0.7070 (ttpp) cc_final: 0.6705 (tmmt) REVERT: G 159 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7769 (m) REVERT: I 85 GLU cc_start: 0.7635 (pt0) cc_final: 0.7164 (pm20) REVERT: I 88 VAL cc_start: 0.6151 (OUTLIER) cc_final: 0.5935 (m) REVERT: I 106 GLU cc_start: 0.8316 (mp0) cc_final: 0.7898 (mp0) REVERT: I 181 GLN cc_start: 0.8903 (tp40) cc_final: 0.8592 (tp40) REVERT: I 238 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: I 317 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7975 (mtp180) REVERT: I 421 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7880 (mmt) REVERT: I 487 MET cc_start: 0.7987 (tpt) cc_final: 0.7766 (tpp) REVERT: I 537 LYS cc_start: 0.9216 (tptp) cc_final: 0.8705 (tptp) REVERT: I 643 LYS cc_start: 0.9216 (mtpm) cc_final: 0.8922 (mttp) REVERT: I 682 LYS cc_start: 0.6776 (mppt) cc_final: 0.6463 (mmtm) REVERT: I 719 GLU cc_start: 0.7153 (tp30) cc_final: 0.6865 (tp30) REVERT: J 36 LYS cc_start: 0.9232 (tttm) cc_final: 0.8994 (tttt) REVERT: S 84 ASN cc_start: 0.8960 (m-40) cc_final: 0.8626 (m110) REVERT: S 135 ASN cc_start: 0.8573 (t0) cc_final: 0.8214 (t0) REVERT: Y 263 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5294 (ppp) REVERT: Y 614 MET cc_start: 0.4919 (tpt) cc_final: 0.4609 (tpt) outliers start: 64 outliers final: 39 residues processed: 563 average time/residue: 0.8229 time to fit residues: 555.5965 Evaluate side-chains 576 residues out of total 4294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 519 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1047 ARG Chi-restraints excluded: chain B residue 1151 LYS Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 566 LEU Chi-restraints excluded: chain I residue 579 VAL Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 152 ILE Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 208 HIS Chi-restraints excluded: chain Y residue 263 MET Chi-restraints excluded: chain Y residue 428 GLN Chi-restraints excluded: chain Y residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 162 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 165 optimal weight: 0.4980 chunk 126 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN B 101 ASN B 371 HIS B 481 GLN B 645 GLN C 229 ASN ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Y 55 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092164 restraints weight = 56282.804| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.06 r_work: 0.2813 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40457 Z= 0.136 Angle : 0.585 13.266 54985 Z= 0.305 Chirality : 0.044 0.205 6243 Planarity : 0.004 0.052 6674 Dihedral : 13.231 160.202 5965 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 15.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.12), residues: 4633 helix: 1.20 (0.12), residues: 1822 sheet: -0.16 (0.20), residues: 640 loop : -0.37 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 466 TYR 0.023 0.001 TYR B 15 PHE 0.029 0.001 PHE A 938 TRP 0.012 0.001 TRP A 365 HIS 0.008 0.001 HIS Y 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (40442) covalent geometry : angle 0.58233 / 0.30 (54970) hydrogen bonds : bond 0.03892 / 2.53 ( 1761) hydrogen bonds : angle 4.49606 / 3.12 ( 4927) metal coordination : bond 0.00585 / 0.44 ( 15) metal coordination : angle 3.71400 / 1.99 ( 15) =============================================================================== Job complete usr+sys time: 18294.11 seconds wall clock time: 311 minutes 44.28 seconds (18704.28 seconds total)