Starting phenix.real_space_refine on Sun Jul 5 18:30:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205.map" model { file = "/net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p5x_13205/07_2026/7p5x_13205_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.084 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 86 5.49 5 S 97 5.16 5 C 18173 2.51 5 N 5257 2.21 5 O 5850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29465 Number of models: 1 Model: "" Number of chains: 12 Chain: "AA" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "AB" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1790 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Chain: "AC" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8678 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 59, 'TRANS': 1061} Chain: "AD" Number of atoms: 9897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 9897 Classifications: {'peptide': 1265} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1207} Chain breaks: 2 Chain: "AE" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 684 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "AF" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2543 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "AJ" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 726 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 7, 'TRANS': 81} Chain: "AO" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 879 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "AP" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 884 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "AX" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 808 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "AY" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 866 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "AD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19247 SG CYSAD 890 21.599 114.720 85.254 1.00 49.51 S ATOM 19809 SG CYSAD 967 24.953 114.169 87.022 1.00 45.09 S ATOM 19851 SG CYSAD 974 23.977 112.217 83.842 1.00 38.31 S ATOM 19870 SG CYSAD 977 24.895 115.817 83.603 1.00 41.89 S ATOM 12674 SG CYSAD 60 47.318 62.781 122.393 1.00 81.43 S ATOM 12692 SG CYSAD 62 48.768 62.030 125.791 1.00 84.40 S ATOM 12801 SG CYSAD 75 45.040 62.474 125.518 1.00 83.03 S ATOM 12827 SG CYSAD 78 47.279 65.463 125.136 1.00 79.51 S Time building chain proxies: 6.03, per 1000 atoms: 0.20 Number of scatterers: 29465 At special positions: 0 Unit cell: (129.36, 165.48, 192.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 86 15.00 O 5850 8.00 N 5257 7.00 C 18173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNAD2000 " pdb="ZN ZNAD2000 " - pdb=" SG CYSAD 974 " pdb="ZN ZNAD2000 " - pdb=" SG CYSAD 977 " pdb="ZN ZNAD2000 " - pdb=" SG CYSAD 890 " pdb="ZN ZNAD2000 " - pdb=" SG CYSAD 967 " pdb=" ZNAD2001 " pdb="ZN ZNAD2001 " - pdb=" SG CYSAD 62 " pdb="ZN ZNAD2001 " - pdb=" SG CYSAD 78 " pdb="ZN ZNAD2001 " - pdb=" SG CYSAD 75 " pdb="ZN ZNAD2001 " - pdb=" SG CYSAD 60 " Number of angles added : 12 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 43.9% alpha, 14.6% beta 27 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'AA' and resid 30 through 45 Processing helix chain 'AA' and resid 72 through 81 Processing helix chain 'AA' and resid 151 through 156 removed outlier: 3.690A pdb=" N SERAA 155 " --> pdb=" O GLNAA 151 " (cutoff:3.500A) Processing helix chain 'AA' and resid 203 through 225 removed outlier: 3.645A pdb=" N ARGAA 223 " --> pdb=" O PHEAA 219 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEUAA 225 " --> pdb=" O LEUAA 221 " (cutoff:3.500A) Processing helix chain 'AB' and resid 29 through 45 removed outlier: 4.275A pdb=" N THRAB 33 " --> pdb=" O GLYAB 29 " (cutoff:3.500A) Processing helix chain 'AB' and resid 72 through 82 removed outlier: 3.504A pdb=" N GLYAB 82 " --> pdb=" O LEUAB 78 " (cutoff:3.500A) Processing helix chain 'AB' and resid 108 through 110 No H-bonds generated for 'chain 'AB' and resid 108 through 110' Processing helix chain 'AB' and resid 203 through 224 Processing helix chain 'AC' and resid 45 through 57 removed outlier: 4.144A pdb=" N SERAC 51 " --> pdb=" O VALAC 47 " (cutoff:3.500A) Processing helix chain 'AC' and resid 58 through 68 Processing helix chain 'AC' and resid 75 through 85 Processing helix chain 'AC' and resid 109 through 117 Processing helix chain 'AC' and resid 225 through 232 Processing helix chain 'AC' and resid 235 through 243 Processing helix chain 'AC' and resid 247 through 255 Processing helix chain 'AC' and resid 261 through 273 Processing helix chain 'AC' and resid 279 through 292 removed outlier: 3.876A pdb=" N ALAAC 283 " --> pdb=" O THRAC 279 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLNAC 284 " --> pdb=" O LYSAC 280 " (cutoff:3.500A) Processing helix chain 'AC' and resid 300 through 312 Processing helix chain 'AC' and resid 325 through 342 Processing helix chain 'AC' and resid 371 through 396 removed outlier: 3.928A pdb=" N THRAC 396 " --> pdb=" O ARGAC 392 " (cutoff:3.500A) Processing helix chain 'AC' and resid 404 through 408 Processing helix chain 'AC' and resid 411 through 425 removed outlier: 3.555A pdb=" N VALAC 415 " --> pdb=" O ILEAC 411 " (cutoff:3.500A) Processing helix chain 'AC' and resid 435 through 444 removed outlier: 3.515A pdb=" N GLYAC 439 " --> pdb=" O ASNAC 435 " (cutoff:3.500A) Processing helix chain 'AC' and resid 467 through 471 removed outlier: 4.011A pdb=" N TYRAC 471 " --> pdb=" O PROAC 468 " (cutoff:3.500A) Processing helix chain 'AC' and resid 523 through 530 removed outlier: 3.758A pdb=" N ARGAC 529 " --> pdb=" O ASPAC 525 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HISAC 530 " --> pdb=" O GLUAC 526 " (cutoff:3.500A) Processing helix chain 'AC' and resid 581 through 585 removed outlier: 3.659A pdb=" N ILEAC 585 " --> pdb=" O THRAC 582 " (cutoff:3.500A) Processing helix chain 'AC' and resid 587 through 591 Processing helix chain 'AC' and resid 592 through 604 Processing helix chain 'AC' and resid 622 through 630 removed outlier: 3.695A pdb=" N GLYAC 630 " --> pdb=" O ALAAC 626 " (cutoff:3.500A) Processing helix chain 'AC' and resid 730 through 735 Processing helix chain 'AC' and resid 770 through 774 removed outlier: 4.413A pdb=" N ASPAC 774 " --> pdb=" O VALAC 771 " (cutoff:3.500A) Processing helix chain 'AC' and resid 806 through 817 Processing helix chain 'AC' and resid 847 through 849 No H-bonds generated for 'chain 'AC' and resid 847 through 849' Processing helix chain 'AC' and resid 891 through 895 removed outlier: 3.539A pdb=" N METAC 895 " --> pdb=" O VALAC 892 " (cutoff:3.500A) Processing helix chain 'AC' and resid 919 through 932 Processing helix chain 'AC' and resid 944 through 948 Processing helix chain 'AC' and resid 951 through 954 Processing helix chain 'AC' and resid 972 through 982 Processing helix chain 'AC' and resid 1027 through 1031 Processing helix chain 'AC' and resid 1050 through 1054 Processing helix chain 'AC' and resid 1060 through 1071 Processing helix chain 'AC' and resid 1072 through 1082 removed outlier: 3.544A pdb=" N LEUAC1076 " --> pdb=" O ALAAC1072 " (cutoff:3.500A) Processing helix chain 'AC' and resid 1086 through 1100 removed outlier: 3.946A pdb=" N VALAC1091 " --> pdb=" O THRAC1087 " (cutoff:3.500A) Processing helix chain 'AC' and resid 1109 through 1121 removed outlier: 3.859A pdb=" N LYSAC1113 " --> pdb=" O PROAC1109 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 7 Processing helix chain 'AD' and resid 16 through 23 Processing helix chain 'AD' and resid 48 through 53 Processing helix chain 'AD' and resid 84 through 90 removed outlier: 3.748A pdb=" N VALAD 87 " --> pdb=" O ARGAD 84 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGAD 88 " --> pdb=" O ALAAD 85 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARGAD 89 " --> pdb=" O LYSAD 86 " (cutoff:3.500A) Processing helix chain 'AD' and resid 112 through 119 Processing helix chain 'AD' and resid 121 through 130 Processing helix chain 'AD' and resid 140 through 147 Processing helix chain 'AD' and resid 147 through 187 Processing helix chain 'AD' and resid 190 through 228 removed outlier: 3.555A pdb=" N ARGAD 194 " --> pdb=" O LYSAD 190 " (cutoff:3.500A) Processing helix chain 'AD' and resid 237 through 248 Processing helix chain 'AD' and resid 257 through 268 Processing helix chain 'AD' and resid 269 through 284 Processing helix chain 'AD' and resid 286 through 305 removed outlier: 3.903A pdb=" N LEUAD 290 " --> pdb=" O GLYAD 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARGAD 291 " --> pdb=" O GLNAD 287 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SERAD 305 " --> pdb=" O ALAAD 301 " (cutoff:3.500A) Processing helix chain 'AD' and resid 308 through 311 Processing helix chain 'AD' and resid 321 through 325 Processing helix chain 'AD' and resid 339 through 361 removed outlier: 3.990A pdb=" N LEUAD 343 " --> pdb=" O ASPAD 339 " (cutoff:3.500A) Processing helix chain 'AD' and resid 363 through 383 Processing helix chain 'AD' and resid 401 through 407 Processing helix chain 'AD' and resid 411 through 417 Processing helix chain 'AD' and resid 445 through 463 Proline residue: AD 454 - end of helix removed outlier: 3.556A pdb=" N LYSAD 458 " --> pdb=" O PROAD 454 " (cutoff:3.500A) Processing helix chain 'AD' and resid 468 through 479 Processing helix chain 'AD' and resid 480 through 491 removed outlier: 4.231A pdb=" N TRPAD 484 " --> pdb=" O ARGAD 480 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASPAD 485 " --> pdb=" O PROAD 481 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VALAD 486 " --> pdb=" O GLNAD 482 " (cutoff:3.500A) Processing helix chain 'AD' and resid 505 through 507 No H-bonds generated for 'chain 'AD' and resid 505 through 507' Processing helix chain 'AD' and resid 525 through 527 No H-bonds generated for 'chain 'AD' and resid 525 through 527' Processing helix chain 'AD' and resid 528 through 533 Processing helix chain 'AD' and resid 548 through 558 Processing helix chain 'AD' and resid 579 through 590 removed outlier: 3.622A pdb=" N THRAD 589 " --> pdb=" O LEUAD 585 " (cutoff:3.500A) Processing helix chain 'AD' and resid 614 through 623 Processing helix chain 'AD' and resid 646 through 651 Processing helix chain 'AD' and resid 666 through 676 Processing helix chain 'AD' and resid 688 through 703 Processing helix chain 'AD' and resid 704 through 724 removed outlier: 3.894A pdb=" N THRAD 724 " --> pdb=" O PHEAD 720 " (cutoff:3.500A) Processing helix chain 'AD' and resid 740 through 761 Processing helix chain 'AD' and resid 765 through 792 removed outlier: 3.513A pdb=" N ARGAD 769 " --> pdb=" O ASNAD 765 " (cutoff:3.500A) Processing helix chain 'AD' and resid 796 through 804 removed outlier: 3.866A pdb=" N ILEAD 801 " --> pdb=" O PROAD 797 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VALAD 802 " --> pdb=" O ILEAD 798 " (cutoff:3.500A) Processing helix chain 'AD' and resid 809 through 817 removed outlier: 3.553A pdb=" N THRAD 813 " --> pdb=" O ASNAD 809 " (cutoff:3.500A) Processing helix chain 'AD' and resid 844 through 880 removed outlier: 3.930A pdb=" N ALAAD 863 " --> pdb=" O LEUAD 859 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEUAD 864 " --> pdb=" O ALAAD 860 " (cutoff:3.500A) Processing helix chain 'AD' and resid 944 through 954 Processing helix chain 'AD' and resid 975 through 979 Processing helix chain 'AD' and resid 993 through 1004 removed outlier: 3.624A pdb=" N VALAD 997 " --> pdb=" O ALAAD 993 " (cutoff:3.500A) Processing helix chain 'AD' and resid 1005 through 1007 No H-bonds generated for 'chain 'AD' and resid 1005 through 1007' Processing helix chain 'AD' and resid 1028 through 1037 Processing helix chain 'AD' and resid 1118 through 1126 Processing helix chain 'AD' and resid 1127 through 1145 removed outlier: 3.550A pdb=" N ALAAD1145 " --> pdb=" O GLUAD1141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 1151 through 1161 removed outlier: 4.239A pdb=" N ILEAD1155 " --> pdb=" O HISAD1151 " (cutoff:3.500A) Processing helix chain 'AD' and resid 1184 through 1196 removed outlier: 3.528A pdb=" N ALAAD1196 " --> pdb=" O ARGAD1192 " (cutoff:3.500A) Processing helix chain 'AD' and resid 1210 through 1217 Processing helix chain 'AD' and resid 1220 through 1228 Processing helix chain 'AD' and resid 1229 through 1241 Processing helix chain 'AD' and resid 1248 through 1256 Processing helix chain 'AD' and resid 1261 through 1264 Processing helix chain 'AD' and resid 1265 through 1270 Processing helix chain 'AD' and resid 1276 through 1283 Processing helix chain 'AE' and resid 30 through 34 Processing helix chain 'AE' and resid 36 through 44 Processing helix chain 'AE' and resid 46 through 66 Processing helix chain 'AE' and resid 87 through 98 Processing helix chain 'AF' and resid 149 through 159 Processing helix chain 'AF' and resid 164 through 176 removed outlier: 4.353A pdb=" N VALAF 176 " --> pdb=" O GLNAF 172 " (cutoff:3.500A) Processing helix chain 'AF' and resid 182 through 206 removed outlier: 3.576A pdb=" N GLUAF 206 " --> pdb=" O ALAAF 202 " (cutoff:3.500A) Processing helix chain 'AF' and resid 212 through 237 Processing helix chain 'AF' and resid 239 through 247 removed outlier: 4.249A pdb=" N ARGAF 247 " --> pdb=" O SERAF 243 " (cutoff:3.500A) Processing helix chain 'AF' and resid 254 through 272 Processing helix chain 'AF' and resid 280 through 300 removed outlier: 4.375A pdb=" N TYRAF 284 " --> pdb=" O LYSAF 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THRAF 286 " --> pdb=" O SERAF 282 " (cutoff:3.500A) Processing helix chain 'AF' and resid 307 through 329 removed outlier: 3.806A pdb=" N VALAF 313 " --> pdb=" O HISAF 309 " (cutoff:3.500A) Processing helix chain 'AF' and resid 333 through 341 Processing helix chain 'AF' and resid 346 through 355 Processing helix chain 'AF' and resid 372 through 376 Processing helix chain 'AF' and resid 386 through 403 Processing helix chain 'AF' and resid 406 through 417 Processing helix chain 'AF' and resid 426 through 435 Processing helix chain 'AF' and resid 437 through 453 Processing helix chain 'AF' and resid 454 through 463 removed outlier: 5.757A pdb=" N VALAF 460 " --> pdb=" O SERAF 456 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEUAF 461 " --> pdb=" O ARGAF 457 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASPAF 463 " --> pdb=" O GLNAF 459 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 89 Processing helix chain 'AJ' and resid 90 through 111 Processing helix chain 'AX' and resid 4 through 21 Proline residue: AX 16 - end of helix Processing helix chain 'AX' and resid 25 through 33 removed outlier: 3.529A pdb=" N ALAAX 29 " --> pdb=" O THRAX 25 " (cutoff:3.500A) Processing helix chain 'AX' and resid 37 through 48 removed outlier: 3.921A pdb=" N ASPAX 41 " --> pdb=" O GLYAX 37 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALAAX 42 " --> pdb=" O LYSAX 38 " (cutoff:3.500A) Processing helix chain 'AX' and resid 87 through 99 Processing helix chain 'AX' and resid 110 through 122 Processing helix chain 'AY' and resid 4 through 19 Processing helix chain 'AY' and resid 24 through 32 Processing helix chain 'AY' and resid 40 through 59 Processing helix chain 'AY' and resid 91 through 100 Processing helix chain 'AY' and resid 107 through 124 Processing sheet with id=AA1, first strand: chain 'AA' and resid 8 through 13 removed outlier: 6.622A pdb=" N ASPAA 190 " --> pdb=" O PROAA 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 110 through 111 removed outlier: 3.849A pdb=" N TYRAA 96 " --> pdb=" O VALAA 111 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLUAA 135 " --> pdb=" O ILEAA 56 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILEAA 56 " --> pdb=" O GLUAA 135 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLUAA 137 " --> pdb=" O ILEAA 54 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILEAA 54 " --> pdb=" O GLUAA 137 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VALAA 139 " --> pdb=" O THRAA 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AA' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'AA' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'AA' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'AB' and resid 8 through 10 removed outlier: 6.610A pdb=" N ARGAB 18 " --> pdb=" O VALAB 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AB' and resid 8 through 10 removed outlier: 6.604A pdb=" N ASPAB 190 " --> pdb=" O PROAB 25 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHEAB 189 " --> pdb=" O THRAB 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AB' and resid 93 through 100 removed outlier: 7.277A pdb=" N GLUAB 135 " --> pdb=" O ILEAB 56 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILEAB 56 " --> pdb=" O GLUAB 135 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLUAB 137 " --> pdb=" O ILEAB 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILEAB 54 " --> pdb=" O GLUAB 137 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VALAB 139 " --> pdb=" O THRAB 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AB' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'AB' and resid 103 through 106 removed outlier: 3.769A pdb=" N GLYAB 103 " --> pdb=" O LEUAB 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALAAB 126 " --> pdb=" O VALAB 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AB' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'AC' and resid 30 through 31 removed outlier: 6.642A pdb=" N VALAC 30 " --> pdb=" O ALAAC 964 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'AC' and resid 87 through 88 removed outlier: 6.713A pdb=" N PHEAC 125 " --> pdb=" O PROAC 101 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHEAC 103 " --> pdb=" O PROAC 123 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALAAC 122 " --> pdb=" O ASPAC 147 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASPAC 147 " --> pdb=" O ALAAC 122 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEUAC 124 " --> pdb=" O METAC 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'AC' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'AC' and resid 367 through 370 removed outlier: 6.297A pdb=" N SERAC 168 " --> pdb=" O SERAC 447 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'AC' and resid 175 through 182 removed outlier: 4.150A pdb=" N HISAC 191 " --> pdb=" O VALAC 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEUAC 203 " --> pdb=" O VALAC 195 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLUAC 204 " --> pdb=" O ARGAC 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'AC' and resid 345 through 346 Processing sheet with id=AB9, first strand: chain 'AC' and resid 496 through 497 removed outlier: 5.192A pdb=" N GLNAC 518 " --> pdb=" O LYSAC 509 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLUAC 511 " --> pdb=" O THRAC 516 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THRAC 516 " --> pdb=" O GLUAC 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'AC' and resid 496 through 497 Processing sheet with id=AC2, first strand: chain 'AC' and resid 532 through 533 removed outlier: 4.660A pdb=" N GLUAC 558 " --> pdb=" O LYSAC 554 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'AC' and resid 633 through 634 removed outlier: 6.618A pdb=" N VALAC 633 " --> pdb=" O ILEAC 693 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AC' and resid 659 through 662 removed outlier: 6.972A pdb=" N TYRAC 648 " --> pdb=" O VALAC 644 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VALAC 644 " --> pdb=" O TYRAC 648 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THRAC 650 " --> pdb=" O GLUAC 642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AC' and resid 667 through 668 removed outlier: 3.607A pdb=" N ALAAC 667 " --> pdb=" O ALAAC 675 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'AC' and resid 699 through 700 Processing sheet with id=AC7, first strand: chain 'AC' and resid 998 through 999 removed outlier: 7.077A pdb=" N ILEAC 726 " --> pdb=" O GLYAC 887 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILEAC 889 " --> pdb=" O ILEAC 726 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEUAC 728 " --> pdb=" O ILEAC 889 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILEAC 727 " --> pdb=" O ILEAC 907 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ILEAC 906 " --> pdb=" O ASNAC 709 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEUAC 711 " --> pdb=" O ILEAC 906 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEUAC 908 " --> pdb=" O LEUAC 711 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALAAC 713 " --> pdb=" O LEUAC 908 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THRAC1015 " --> pdb=" O ILEAC 714 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'AC' and resid 740 through 751 removed outlier: 3.679A pdb=" N GLYAC 840 " --> pdb=" O TYRAC 863 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALAAC 865 " --> pdb=" O VALAC 838 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VALAC 838 " --> pdb=" O ALAAC 865 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LYSAC 867 " --> pdb=" O GLYAC 836 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLYAC 836 " --> pdb=" O LYSAC 867 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AC' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'AC' and resid 792 through 794 removed outlier: 6.592A pdb=" N LEUAC 828 " --> pdb=" O LEUAC 793 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'AC' and resid 935 through 936 Processing sheet with id=AD3, first strand: chain 'AC' and resid 1033 through 1035 Processing sheet with id=AD4, first strand: chain 'AC' and resid 1057 through 1059 removed outlier: 3.753A pdb=" N GLNAC1057 " --> pdb=" O VALAD 422 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'AC' and resid 1127 through 1129 Processing sheet with id=AD6, first strand: chain 'AD' and resid 24 through 27 removed outlier: 7.684A pdb=" N HISAD 94 " --> pdb=" O TYRAD 25 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLUAD 27 " --> pdb=" O HISAD 94 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLUAD 96 " --> pdb=" O GLUAD 27 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N LEUAD 97 " --> pdb=" O PROAD 318 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ALAAD 99 " --> pdb=" O ALAAD 316 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALAAD 316 " --> pdb=" O ALAAD 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'AD' and resid 234 through 235 removed outlier: 7.104A pdb=" N THRAD 253 " --> pdb=" O THRAD 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AD' and resid 328 through 329 removed outlier: 3.525A pdb=" N VALAD 328 " --> pdb=" O ALAAD 336 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHEAD 335 " --> pdb=" O ILEAF 359 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'AD' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'AD' and resid 885 through 887 Processing sheet with id=AE2, first strand: chain 'AD' and resid 896 through 899 Processing sheet with id=AE3, first strand: chain 'AD' and resid 1076 through 1077 Processing sheet with id=AE4, first strand: chain 'AD' and resid 1181 through 1183 removed outlier: 4.611A pdb=" N ARGAD1165 " --> pdb=" O VALAD1207 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'AD' and resid 1272 through 1275 Processing sheet with id=AE6, first strand: chain 'AJ' and resid 39 through 45 Processing sheet with id=AE7, first strand: chain 'AY' and resid 63 through 68 removed outlier: 7.696A pdb=" N THRAY 73 " --> pdb=" O VALAY 67 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5444 1.32 - 1.45: 7267 1.45 - 1.57: 17070 1.57 - 1.69: 170 1.69 - 1.81: 173 Bond restraints: 30124 Sorted by residual: bond pdb=" CA TRPAY 70 " pdb=" CB TRPAY 70 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.46e-02 4.69e+03 1.48e+01 bond pdb=" CA TRPAY 70 " pdb=" C TRPAY 70 " ideal model delta sigma weight residual 1.524 1.468 0.057 1.48e-02 4.57e+03 1.46e+01 bond pdb=" CB TRPAY 70 " pdb=" CG TRPAY 70 " ideal model delta sigma weight residual 1.498 1.393 0.105 3.10e-02 1.04e+03 1.14e+01 bond pdb=" O3' DGAP 124 " pdb=" P DTAP 125 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.08e+01 bond pdb=" C3' DGAP 107 " pdb=" C2' DGAP 107 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 30119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 40117 1.42 - 2.83: 868 2.83 - 4.25: 130 4.25 - 5.67: 33 5.67 - 7.09: 15 Bond angle restraints: 41163 Sorted by residual: angle pdb=" N PROAX 103 " pdb=" CA PROAX 103 " pdb=" CB PROAX 103 " ideal model delta sigma weight residual 103.31 110.40 -7.09 8.90e-01 1.26e+00 6.34e+01 angle pdb=" N PROAY 87 " pdb=" CA PROAY 87 " pdb=" CB PROAY 87 " ideal model delta sigma weight residual 103.35 109.95 -6.60 8.70e-01 1.32e+00 5.75e+01 angle pdb=" N PROAY 86 " pdb=" CA PROAY 86 " pdb=" CB PROAY 86 " ideal model delta sigma weight residual 103.08 109.86 -6.78 9.70e-01 1.06e+00 4.89e+01 angle pdb=" N VALAY 67 " pdb=" CA VALAY 67 " pdb=" C VALAY 67 " ideal model delta sigma weight residual 110.42 104.88 5.54 9.40e-01 1.13e+00 3.48e+01 angle pdb=" N PROAY 108 " pdb=" CA PROAY 108 " pdb=" CB PROAY 108 " ideal model delta sigma weight residual 103.33 109.77 -6.44 1.10e+00 8.26e-01 3.43e+01 ... (remaining 41158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 17776 34.79 - 69.57: 436 69.57 - 104.36: 13 104.36 - 139.15: 2 139.15 - 173.94: 1 Dihedral angle restraints: 18228 sinusoidal: 7949 harmonic: 10279 Sorted by residual: dihedral pdb=" N SERAY 72 " pdb=" C SERAY 72 " pdb=" CA SERAY 72 " pdb=" CB SERAY 72 " ideal model delta harmonic sigma weight residual 122.80 135.38 -12.58 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" C SERAY 72 " pdb=" N SERAY 72 " pdb=" CA SERAY 72 " pdb=" CB SERAY 72 " ideal model delta harmonic sigma weight residual -122.60 -132.64 10.04 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C4' DAAP 105 " pdb=" C3' DAAP 105 " pdb=" O3' DAAP 105 " pdb=" P DAAP 106 " ideal model delta sinusoidal sigma weight residual -140.00 33.94 -173.94 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4427 0.092 - 0.184: 262 0.184 - 0.275: 7 0.275 - 0.367: 2 0.367 - 0.459: 1 Chirality restraints: 4699 Sorted by residual: chirality pdb=" CA SERAY 72 " pdb=" N SERAY 72 " pdb=" C SERAY 72 " pdb=" CB SERAY 72 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA VALAX 72 " pdb=" N VALAX 72 " pdb=" C VALAX 72 " pdb=" CB VALAX 72 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PROAX 108 " pdb=" N PROAX 108 " pdb=" C PROAX 108 " pdb=" CB PROAX 108 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4696 not shown) Planarity restraints: 5121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRAC 404 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PROAC 405 " -0.118 5.00e-02 4.00e+02 pdb=" CA PROAC 405 " 0.035 5.00e-02 4.00e+02 pdb=" CD PROAC 405 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRAF 333 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.10e+00 pdb=" N PROAF 334 " -0.107 5.00e-02 4.00e+02 pdb=" CA PROAF 334 " 0.032 5.00e-02 4.00e+02 pdb=" CD PROAF 334 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLYAY 65 " -0.013 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C GLYAY 65 " 0.042 2.00e-02 2.50e+03 pdb=" O GLYAY 65 " -0.016 2.00e-02 2.50e+03 pdb=" N ARGAY 66 " -0.014 2.00e-02 2.50e+03 ... (remaining 5118 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2926 2.75 - 3.28: 27594 3.28 - 3.82: 47098 3.82 - 4.36: 56792 4.36 - 4.90: 99690 Nonbonded interactions: 234100 Sorted by model distance: nonbonded pdb=" O SERAC 173 " pdb=" OH TYRAC 177 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THRAF 333 " pdb=" OE1 GLUAF 336 " model vdw 2.207 3.040 nonbonded pdb=" NE ARGAD 37 " pdb=" OG SERAY 72 " model vdw 2.208 3.120 nonbonded pdb=" O LYSAC 509 " pdb=" OG1 THRAC 516 " model vdw 2.221 3.040 nonbonded pdb=" OG SERAD1173 " pdb=" O GLUAD1200 " model vdw 2.225 3.040 ... (remaining 234095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AA' selection = (chain 'AB' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 30132 Z= 0.226 Angle : 0.530 7.087 41175 Z= 0.352 Chirality : 0.044 0.459 4699 Planarity : 0.004 0.068 5121 Dihedral : 13.286 173.937 11608 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.73 % Allowed : 4.17 % Favored : 94.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.23 % 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: 0.69 (0.14), residues: 3566 helix: 1.97 (0.14), residues: 1425 sheet: 0.52 (0.28), residues: 362 loop : -0.85 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAY 66 TYR 0.012 0.001 TYRAD 586 PHE 0.012 0.001 PHEAC 897 TRP 0.014 0.001 TRPAY 70 HIS 0.005 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.23 (30124) covalent geometry : angle 0.52858 / 0.35 (41163) hydrogen bonds : bond 0.15156 / 10.10 ( 1372) hydrogen bonds : angle 5.57883 / 4.02 ( 3852) metal coordination : bond 0.00418 / 0.18 ( 8) metal coordination : angle 2.03294 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: AB 95 MET cc_start: 0.8257 (mtm) cc_final: 0.7983 (mtp) REVERT: AC 210 ARG cc_start: 0.7667 (mpp80) cc_final: 0.7403 (mtt90) REVERT: AC 976 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8170 (tt) REVERT: AD 241 TYR cc_start: 0.8058 (t80) cc_final: 0.7720 (t80) REVERT: AD 742 GLN cc_start: 0.7632 (mt0) cc_final: 0.7368 (tt0) REVERT: AF 339 LYS cc_start: 0.8369 (mppt) cc_final: 0.8143 (mptt) REVERT: AJ 82 TRP cc_start: 0.7883 (t-100) cc_final: 0.7618 (t-100) REVERT: AJ 87 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7013 (tp30) REVERT: AY 8 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (mtm180) REVERT: AY 58 LEU cc_start: 0.7402 (mt) cc_final: 0.7199 (tt) REVERT: AY 70 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7142 (m-10) outliers start: 51 outliers final: 25 residues processed: 410 average time/residue: 0.1959 time to fit residues: 125.2234 Evaluate side-chains 311 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AC residue 1035 ARG Chi-restraints excluded: chain AD residue 590 THR Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 71 GLU Chi-restraints excluded: chain AY residue 8 ARG Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 70 TRP Chi-restraints excluded: chain AY residue 72 SER Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0000 chunk 298 optimal weight: 2.9990 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AB 100 GLN AD 369 ASN ** AD 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD1247 ASN AF 237 ASN AF 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116174 restraints weight = 37270.504| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.02 r_work: 0.3001 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30132 Z= 0.114 Angle : 0.490 8.192 41175 Z= 0.268 Chirality : 0.041 0.200 4699 Planarity : 0.004 0.060 5121 Dihedral : 14.940 173.427 4913 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 7.18 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.88 (0.14), residues: 3566 helix: 2.11 (0.14), residues: 1461 sheet: 0.52 (0.28), residues: 374 loop : -0.76 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAC1139 TYR 0.013 0.001 TYRAF 196 PHE 0.014 0.001 PHEAC 561 TRP 0.008 0.001 TRPAC 929 HIS 0.004 0.001 HISAD 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (30124) covalent geometry : angle 0.48843 / 0.27 (41163) hydrogen bonds : bond 0.04518 / 3.12 ( 1372) hydrogen bonds : angle 4.31583 / 3.11 ( 3852) metal coordination : bond 0.00442 / 0.22 ( 8) metal coordination : angle 2.42675 / 1.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: AC 1020 TYR cc_start: 0.9300 (t80) cc_final: 0.9069 (t80) REVERT: AD 76 GLU cc_start: 0.7787 (pm20) cc_final: 0.7510 (pm20) REVERT: AD 241 TYR cc_start: 0.8460 (t80) cc_final: 0.8109 (t80) REVERT: AD 742 GLN cc_start: 0.8159 (mt0) cc_final: 0.7956 (tt0) REVERT: AF 295 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7882 (ttt90) REVERT: AF 339 LYS cc_start: 0.8104 (mppt) cc_final: 0.7817 (tttp) REVERT: AF 409 GLU cc_start: 0.7752 (mp0) cc_final: 0.7424 (mt-10) REVERT: AJ 87 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7263 (tp30) outliers start: 48 outliers final: 32 residues processed: 335 average time/residue: 0.2078 time to fit residues: 110.4423 Evaluate side-chains 305 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 122 ASP Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 246 ASP Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 71 ASP Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 22 optimal weight: 0.0970 chunk 94 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 235 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AC 442 HIS ** AD 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD1247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114292 restraints weight = 37331.420| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.27 r_work: 0.2935 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30132 Z= 0.122 Angle : 0.479 7.655 41175 Z= 0.260 Chirality : 0.041 0.195 4699 Planarity : 0.004 0.058 5121 Dihedral : 14.862 172.724 4895 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 7.25 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.91 (0.14), residues: 3566 helix: 2.14 (0.14), residues: 1456 sheet: 0.50 (0.27), residues: 399 loop : -0.74 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAC1139 TYR 0.015 0.001 TYRAF 196 PHE 0.014 0.001 PHEAC 561 TRP 0.008 0.001 TRPAC 929 HIS 0.006 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (30124) covalent geometry : angle 0.47707 / 0.26 (41163) hydrogen bonds : bond 0.04249 / 2.96 ( 1372) hydrogen bonds : angle 4.12703 / 2.96 ( 3852) metal coordination : bond 0.00522 / 0.25 ( 8) metal coordination : angle 2.40921 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: AB 95 MET cc_start: 0.8557 (mtp) cc_final: 0.8339 (mtp) REVERT: AC 519 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9061 (mp) REVERT: AD 241 TYR cc_start: 0.8403 (t80) cc_final: 0.8033 (t80) REVERT: AD 273 GLU cc_start: 0.7758 (tp30) cc_final: 0.7513 (tp30) REVERT: AD 557 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8922 (mp) REVERT: AD 742 GLN cc_start: 0.8160 (mt0) cc_final: 0.7911 (tt0) REVERT: AF 409 GLU cc_start: 0.7655 (mp0) cc_final: 0.7257 (mt-10) REVERT: AJ 87 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7111 (tp30) outliers start: 66 outliers final: 47 residues processed: 340 average time/residue: 0.1937 time to fit residues: 105.2495 Evaluate side-chains 318 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AB residue 2 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 122 ASP Chi-restraints excluded: chain AB residue 129 ASN Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 74 ILE Chi-restraints excluded: chain AD residue 158 GLU Chi-restraints excluded: chain AD residue 246 ASP Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AE residue 72 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 51 ASP Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 71 ASP Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 89 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AC 363 HIS AD1247 ASN AE 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111979 restraints weight = 37120.604| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.18 r_work: 0.2903 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30132 Z= 0.163 Angle : 0.512 8.589 41175 Z= 0.276 Chirality : 0.042 0.171 4699 Planarity : 0.004 0.049 5121 Dihedral : 14.912 171.759 4895 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.64 % Allowed : 7.56 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.80 (0.14), residues: 3566 helix: 2.06 (0.14), residues: 1445 sheet: 0.51 (0.27), residues: 386 loop : -0.82 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAC1139 TYR 0.017 0.001 TYRAC 648 PHE 0.019 0.002 PHEAC 130 TRP 0.009 0.001 TRPAD1221 HIS 0.009 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (30124) covalent geometry : angle 0.50986 / 0.28 (41163) hydrogen bonds : bond 0.04587 / 3.20 ( 1372) hydrogen bonds : angle 4.14246 / 2.96 ( 3852) metal coordination : bond 0.00642 / 0.32 ( 8) metal coordination : angle 2.49973 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: AB 33 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.6937 (t) REVERT: AB 95 MET cc_start: 0.8600 (mtp) cc_final: 0.8390 (mtp) REVERT: AC 519 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9080 (mp) REVERT: AD 241 TYR cc_start: 0.8503 (t80) cc_final: 0.8068 (t80) REVERT: AD 273 GLU cc_start: 0.7816 (tp30) cc_final: 0.7563 (tp30) REVERT: AD 557 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8956 (mp) REVERT: AD 742 GLN cc_start: 0.8242 (mt0) cc_final: 0.7989 (tt0) REVERT: AF 324 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7464 (mm) REVERT: AF 409 GLU cc_start: 0.7779 (mp0) cc_final: 0.7389 (mt-10) REVERT: AF 423 GLN cc_start: 0.7195 (pp30) cc_final: 0.6574 (pt0) REVERT: AJ 87 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7194 (tp30) outliers start: 78 outliers final: 59 residues processed: 350 average time/residue: 0.1998 time to fit residues: 111.4984 Evaluate side-chains 331 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AA residue 159 ILE Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 122 ASP Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 106 VAL Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 74 ILE Chi-restraints excluded: chain AD residue 92 MET Chi-restraints excluded: chain AD residue 158 GLU Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 246 ASP Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 737 VAL Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AE residue 72 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 324 LEU Chi-restraints excluded: chain AF residue 348 VAL Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 70 ILE Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 296 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 210 optimal weight: 0.0670 chunk 327 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AD1247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110217 restraints weight = 37430.856| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.24 r_work: 0.2904 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30132 Z= 0.115 Angle : 0.472 7.137 41175 Z= 0.256 Chirality : 0.041 0.212 4699 Planarity : 0.004 0.050 5121 Dihedral : 14.868 172.216 4895 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 8.30 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.91 (0.14), residues: 3566 helix: 2.16 (0.14), residues: 1445 sheet: 0.58 (0.27), residues: 386 loop : -0.76 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAC1139 TYR 0.016 0.001 TYRAC 648 PHE 0.018 0.001 PHEAC 130 TRP 0.011 0.001 TRPAC 929 HIS 0.004 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (30124) covalent geometry : angle 0.46864 / 0.26 (41163) hydrogen bonds : bond 0.03974 / 2.78 ( 1372) hydrogen bonds : angle 4.02489 / 2.88 ( 3852) metal coordination : bond 0.01125 / 0.57 ( 8) metal coordination : angle 3.51755 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 285 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: AB 95 MET cc_start: 0.8597 (mtp) cc_final: 0.8391 (mtp) REVERT: AC 519 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9066 (mp) REVERT: AD 241 TYR cc_start: 0.8421 (t80) cc_final: 0.7986 (t80) REVERT: AD 273 GLU cc_start: 0.7742 (tp30) cc_final: 0.7444 (tp30) REVERT: AD 557 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8978 (mp) REVERT: AD 742 GLN cc_start: 0.8103 (mt0) cc_final: 0.7832 (tt0) REVERT: AD 1155 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (mm) REVERT: AF 409 GLU cc_start: 0.7672 (mp0) cc_final: 0.7247 (mt-10) REVERT: AJ 87 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7138 (tp30) REVERT: AJ 100 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6645 (mm-30) outliers start: 72 outliers final: 56 residues processed: 344 average time/residue: 0.1935 time to fit residues: 107.1196 Evaluate side-chains 334 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 65 THR Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 158 GLU Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 246 ASP Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AE residue 72 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AD1247 ASN AE 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107529 restraints weight = 37237.937| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.23 r_work: 0.2858 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30132 Z= 0.182 Angle : 0.526 9.145 41175 Z= 0.281 Chirality : 0.043 0.178 4699 Planarity : 0.004 0.052 5121 Dihedral : 14.948 171.229 4895 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.58 % Allowed : 8.61 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.75 (0.14), residues: 3566 helix: 2.01 (0.14), residues: 1445 sheet: 0.45 (0.27), residues: 394 loop : -0.83 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAC 458 TYR 0.018 0.001 TYRAC1020 PHE 0.020 0.002 PHEAC 130 TRP 0.009 0.001 TRPAD1221 HIS 0.010 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (30124) covalent geometry : angle 0.52345 / 0.28 (41163) hydrogen bonds : bond 0.04778 / 3.34 ( 1372) hydrogen bonds : angle 4.11411 / 2.93 ( 3852) metal coordination : bond 0.00991 / 0.49 ( 8) metal coordination : angle 3.23317 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: AB 33 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7495 (t) REVERT: AB 95 MET cc_start: 0.8799 (mtp) cc_final: 0.8584 (mtp) REVERT: AC 519 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9119 (mp) REVERT: AD 241 TYR cc_start: 0.8574 (t80) cc_final: 0.8204 (t80) REVERT: AD 270 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6966 (mt) REVERT: AD 273 GLU cc_start: 0.8020 (tp30) cc_final: 0.7713 (tp30) REVERT: AD 557 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9035 (mp) REVERT: AD 1155 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8791 (mm) REVERT: AF 409 GLU cc_start: 0.7783 (mp0) cc_final: 0.7565 (mp0) REVERT: AF 423 GLN cc_start: 0.7187 (pp30) cc_final: 0.6586 (pt0) REVERT: AJ 87 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7169 (tp30) REVERT: AJ 100 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6674 (mm-30) outliers start: 76 outliers final: 64 residues processed: 338 average time/residue: 0.1865 time to fit residues: 101.1739 Evaluate side-chains 337 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 65 THR Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 9 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 216 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 106 VAL Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 74 ILE Chi-restraints excluded: chain AD residue 92 MET Chi-restraints excluded: chain AD residue 158 GLU Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 270 ILE Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 737 VAL Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1007 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AE residue 72 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 51 ASP Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 57 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 344 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AD1247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109437 restraints weight = 37291.605| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.29 r_work: 0.2877 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30132 Z= 0.122 Angle : 0.479 7.551 41175 Z= 0.259 Chirality : 0.041 0.184 4699 Planarity : 0.004 0.056 5121 Dihedral : 14.869 171.984 4895 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.58 % Allowed : 9.12 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.87 (0.14), residues: 3566 helix: 2.13 (0.14), residues: 1444 sheet: 0.56 (0.27), residues: 386 loop : -0.79 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAC1139 TYR 0.024 0.001 TYRAC 648 PHE 0.018 0.001 PHEAC 130 TRP 0.011 0.001 TRPAC 929 HIS 0.005 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30124) covalent geometry : angle 0.47615 / 0.26 (41163) hydrogen bonds : bond 0.04112 / 2.88 ( 1372) hydrogen bonds : angle 4.01497 / 2.87 ( 3852) metal coordination : bond 0.00588 / 0.29 ( 8) metal coordination : angle 2.87159 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: AB 33 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.6720 (t) REVERT: AB 95 MET cc_start: 0.8607 (mtp) cc_final: 0.8394 (mtp) REVERT: AC 199 ARG cc_start: 0.8233 (tmm160) cc_final: 0.7947 (tmm160) REVERT: AC 519 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9054 (mp) REVERT: AD 241 TYR cc_start: 0.8461 (t80) cc_final: 0.8036 (t80) REVERT: AD 270 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6853 (mt) REVERT: AD 273 GLU cc_start: 0.7760 (tp30) cc_final: 0.7442 (tp30) REVERT: AD 557 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8967 (mp) REVERT: AD 1155 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mm) REVERT: AJ 87 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7114 (tp30) REVERT: AJ 100 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6662 (mm-30) REVERT: AX 21 ASN cc_start: 0.6126 (OUTLIER) cc_final: 0.5556 (p0) outliers start: 76 outliers final: 58 residues processed: 339 average time/residue: 0.1967 time to fit residues: 106.8813 Evaluate side-chains 335 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 65 THR Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 60 LEU Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 216 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 246 ASP Chi-restraints excluded: chain AD residue 270 ILE Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 737 VAL Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AE residue 72 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 21 ASN Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 130 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 197 optimal weight: 0.0170 chunk 254 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 330 optimal weight: 40.0000 chunk 311 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AD 742 GLN AD1247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110325 restraints weight = 37308.635| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.27 r_work: 0.2904 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30132 Z= 0.110 Angle : 0.467 7.111 41175 Z= 0.253 Chirality : 0.040 0.181 4699 Planarity : 0.004 0.057 5121 Dihedral : 14.784 171.920 4895 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 9.66 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.96 (0.14), residues: 3566 helix: 2.20 (0.14), residues: 1445 sheet: 0.58 (0.27), residues: 386 loop : -0.73 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAC1139 TYR 0.017 0.001 TYRAF 196 PHE 0.020 0.001 PHEAC 130 TRP 0.012 0.001 TRPAC 929 HIS 0.004 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (30124) covalent geometry : angle 0.46502 / 0.25 (41163) hydrogen bonds : bond 0.03800 / 2.66 ( 1372) hydrogen bonds : angle 3.93564 / 2.82 ( 3852) metal coordination : bond 0.00554 / 0.27 ( 8) metal coordination : angle 2.43187 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: AC 199 ARG cc_start: 0.8208 (tmm160) cc_final: 0.7926 (tmm160) REVERT: AC 519 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9034 (mp) REVERT: AD 241 TYR cc_start: 0.8435 (t80) cc_final: 0.8140 (t80) REVERT: AD 273 GLU cc_start: 0.7807 (tp30) cc_final: 0.7503 (tp30) REVERT: AD 557 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8964 (mp) REVERT: AD 1155 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8710 (mm) REVERT: AJ 87 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7131 (tp30) REVERT: AJ 100 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6667 (mm-30) REVERT: AX 21 ASN cc_start: 0.6026 (OUTLIER) cc_final: 0.5517 (p0) REVERT: AY 66 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7387 (ttt90) outliers start: 68 outliers final: 54 residues processed: 336 average time/residue: 0.1775 time to fit residues: 95.8546 Evaluate side-chains 334 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 65 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 9 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 216 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 158 GLU Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 21 ASN Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 66 ARG Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 221 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 353 optimal weight: 0.0040 chunk 65 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AD 742 GLN AD1247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109942 restraints weight = 37309.907| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.28 r_work: 0.2888 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30132 Z= 0.122 Angle : 0.478 7.761 41175 Z= 0.258 Chirality : 0.041 0.179 4699 Planarity : 0.004 0.058 5121 Dihedral : 14.792 171.571 4895 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 9.52 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.95 (0.14), residues: 3566 helix: 2.19 (0.14), residues: 1445 sheet: 0.58 (0.27), residues: 386 loop : -0.74 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAC1139 TYR 0.018 0.001 TYRAC 648 PHE 0.020 0.001 PHEAC 130 TRP 0.010 0.001 TRPAC 929 HIS 0.005 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30124) covalent geometry : angle 0.47616 / 0.26 (41163) hydrogen bonds : bond 0.03929 / 2.75 ( 1372) hydrogen bonds : angle 3.94142 / 2.82 ( 3852) metal coordination : bond 0.00570 / 0.28 ( 8) metal coordination : angle 2.48103 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: AC 199 ARG cc_start: 0.8208 (tmm160) cc_final: 0.7929 (tmm160) REVERT: AC 456 ARG cc_start: 0.8046 (ptp90) cc_final: 0.7565 (ptp90) REVERT: AC 519 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9029 (mp) REVERT: AD 241 TYR cc_start: 0.8432 (t80) cc_final: 0.8027 (t80) REVERT: AD 273 GLU cc_start: 0.7783 (tp30) cc_final: 0.7465 (tp30) REVERT: AD 557 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8971 (mp) REVERT: AD 1155 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8692 (mm) REVERT: AJ 87 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7098 (tp30) REVERT: AJ 100 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6587 (mm-30) REVERT: AX 21 ASN cc_start: 0.6146 (OUTLIER) cc_final: 0.5577 (p0) outliers start: 68 outliers final: 57 residues processed: 333 average time/residue: 0.1936 time to fit residues: 102.6918 Evaluate side-chains 336 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 65 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 9 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 216 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AB residue 234 ILE Chi-restraints excluded: chain AC residue 186 THR Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 510 VAL Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 693 ILE Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 781 VAL Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AC residue 1116 LEU Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 629 VAL Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 737 VAL Chi-restraints excluded: chain AD residue 799 ILE Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AX residue 12 LEU Chi-restraints excluded: chain AX residue 21 ASN Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AX residue 72 VAL Chi-restraints excluded: chain AY residue 6 VAL Chi-restraints excluded: chain AY residue 38 SER Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 18 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 253 optimal weight: 0.4980 chunk 143 optimal weight: 0.7980 chunk 196 optimal weight: 0.3980 chunk 148 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AD 742 GLN AD1247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114469 restraints weight = 37107.010| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.22 r_work: 0.2925 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30132 Z= 0.099 Angle : 0.460 7.340 41175 Z= 0.250 Chirality : 0.040 0.174 4699 Planarity : 0.004 0.059 5121 Dihedral : 14.714 171.819 4890 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.90 % Allowed : 9.83 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 1.05 (0.14), residues: 3566 helix: 2.27 (0.14), residues: 1445 sheet: 0.60 (0.27), residues: 387 loop : -0.66 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAD 282 TYR 0.018 0.001 TYRAF 196 PHE 0.020 0.001 PHEAC 130 TRP 0.013 0.001 TRPAC 929 HIS 0.003 0.000 HISAD 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (30124) covalent geometry : angle 0.45842 / 0.25 (41163) hydrogen bonds : bond 0.03529 / 2.47 ( 1372) hydrogen bonds : angle 3.87621 / 2.78 ( 3852) metal coordination : bond 0.00422 / 0.21 ( 8) metal coordination : angle 2.27149 / 1.29 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7132 Ramachandran restraints generated. 3566 Oldfield, 0 Emsley, 3566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: AC 199 ARG cc_start: 0.8272 (tmm160) cc_final: 0.8004 (tmm160) REVERT: AC 456 ARG cc_start: 0.8074 (ptp90) cc_final: 0.7617 (ptp90) REVERT: AC 519 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9092 (mp) REVERT: AD 241 TYR cc_start: 0.8500 (t80) cc_final: 0.8173 (t80) REVERT: AD 273 GLU cc_start: 0.7997 (tp30) cc_final: 0.7660 (tp30) REVERT: AD 557 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8972 (mp) REVERT: AD 1155 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8752 (mm) REVERT: AJ 100 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6564 (mm-30) outliers start: 56 outliers final: 49 residues processed: 335 average time/residue: 0.1850 time to fit residues: 98.9955 Evaluate side-chains 329 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 59 VAL Chi-restraints excluded: chain AA residue 117 THR Chi-restraints excluded: chain AA residue 221 LEU Chi-restraints excluded: chain AB residue 9 LEU Chi-restraints excluded: chain AB residue 33 THR Chi-restraints excluded: chain AB residue 85 VAL Chi-restraints excluded: chain AB residue 93 VAL Chi-restraints excluded: chain AB residue 111 VAL Chi-restraints excluded: chain AB residue 196 VAL Chi-restraints excluded: chain AB residue 216 VAL Chi-restraints excluded: chain AB residue 221 LEU Chi-restraints excluded: chain AC residue 364 PHE Chi-restraints excluded: chain AC residue 519 ILE Chi-restraints excluded: chain AC residue 531 VAL Chi-restraints excluded: chain AC residue 551 MET Chi-restraints excluded: chain AC residue 572 VAL Chi-restraints excluded: chain AC residue 602 MET Chi-restraints excluded: chain AC residue 617 VAL Chi-restraints excluded: chain AC residue 638 THR Chi-restraints excluded: chain AC residue 747 GLU Chi-restraints excluded: chain AC residue 806 THR Chi-restraints excluded: chain AC residue 976 LEU Chi-restraints excluded: chain AC residue 1028 VAL Chi-restraints excluded: chain AC residue 1116 LEU Chi-restraints excluded: chain AD residue 73 ILE Chi-restraints excluded: chain AD residue 162 VAL Chi-restraints excluded: chain AD residue 460 LEU Chi-restraints excluded: chain AD residue 557 ILE Chi-restraints excluded: chain AD residue 605 ASP Chi-restraints excluded: chain AD residue 622 MET Chi-restraints excluded: chain AD residue 705 MET Chi-restraints excluded: chain AD residue 724 THR Chi-restraints excluded: chain AD residue 736 LEU Chi-restraints excluded: chain AD residue 737 VAL Chi-restraints excluded: chain AD residue 823 VAL Chi-restraints excluded: chain AD residue 864 LEU Chi-restraints excluded: chain AD residue 915 VAL Chi-restraints excluded: chain AD residue 971 THR Chi-restraints excluded: chain AD residue 1089 VAL Chi-restraints excluded: chain AD residue 1090 ILE Chi-restraints excluded: chain AD residue 1155 ILE Chi-restraints excluded: chain AD residue 1247 ASN Chi-restraints excluded: chain AF residue 179 LEU Chi-restraints excluded: chain AF residue 323 GLU Chi-restraints excluded: chain AF residue 350 GLU Chi-restraints excluded: chain AF residue 426 THR Chi-restraints excluded: chain AJ residue 24 LEU Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AX residue 33 LEU Chi-restraints excluded: chain AX residue 48 TRP Chi-restraints excluded: chain AX residue 66 VAL Chi-restraints excluded: chain AY residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 154 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 352 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 151 GLN AC 398 GLN AD 742 GLN AD1247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109249 restraints weight = 37433.974| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.29 r_work: 0.2884 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30132 Z= 0.153 Angle : 0.502 8.253 41175 Z= 0.268 Chirality : 0.042 0.170 4699 Planarity : 0.004 0.059 5121 Dihedral : 14.766 171.205 4887 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.03 % Allowed : 9.86 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: 0.93 (0.14), residues: 3566 helix: 2.15 (0.14), residues: 1446 sheet: 0.60 (0.27), residues: 384 loop : -0.73 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGAD 282 TYR 0.016 0.001 TYRAC 648 PHE 0.021 0.001 PHEAC 130 TRP 0.008 0.001 TRPAC 929 HIS 0.007 0.001 HISAD 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (30124) covalent geometry : angle 0.50012 / 0.27 (41163) hydrogen bonds : bond 0.04122 / 2.88 ( 1372) hydrogen bonds : angle 3.94348 / 2.82 ( 3852) metal coordination : bond 0.00687 / 0.35 ( 8) metal coordination : angle 2.42735 / 1.30 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7100.77 seconds wall clock time: 122 minutes 8.88 seconds (7328.88 seconds total)