Starting phenix.real_space_refine on Tue Oct 27 14:03:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ay1_11934/10_2026/7ay1_11934.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.051 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 1 6.06 5 P 58 5.49 5 S 140 5.16 5 C 16003 2.51 5 N 4124 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25186 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8215 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 33, 'TRANS': 999} Chain breaks: 9 Chain: "B" Number of atoms: 8263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8263 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 35, 'TRANS': 997} Chain breaks: 8 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2742 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 5 Chain: "E" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4720 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 22, 'TRANS': 573} Chain breaks: 4 Chain: "S" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Chain: "T" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18333 SG CYS D 440 58.673 96.698 38.120 1.00 31.98 S ATOM 18356 SG CYS D 443 60.164 96.542 35.021 1.00 36.96 S ATOM 18740 SG CYS D 506 62.366 95.952 38.023 1.00 29.69 S ATOM 18763 SG CYS D 509 61.198 99.399 37.162 1.00 28.10 S Time building chain proxies: 4.28, per 1000 atoms: 0.17 Number of scatterers: 25186 At special positions: 0 Unit cell: (124.845, 169.505, 171.535, 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 1 29.99 S 140 16.00 P 58 15.00 O 4860 8.00 N 4124 7.00 C 16003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 469 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 910.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " Number of angles added : 6 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5922 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 24 sheets defined 59.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.969A pdb=" N THR A 178 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 206 removed outlier: 3.643A pdb=" N VAL A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.746A pdb=" N LEU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 249 removed outlier: 3.796A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.842A pdb=" N HIS A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.083A pdb=" N GLY A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.898A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 4.126A pdb=" N LEU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.517A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.600A pdb=" N MET A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.743A pdb=" N TYR A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 433 removed outlier: 3.966A pdb=" N CYS A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 4.003A pdb=" N LEU A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.549A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 492 through 509 Proline residue: A 505 - end of helix removed outlier: 3.760A pdb=" N VAL A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 527 Processing helix chain 'A' and resid 532 through 546 removed outlier: 3.995A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.824A pdb=" N LEU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 3.505A pdb=" N ARG A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.734A pdb=" N MET A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 Processing helix chain 'A' and resid 698 through 714 removed outlier: 4.096A pdb=" N ASP A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 760 removed outlier: 3.832A pdb=" N ILE A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 789 removed outlier: 3.578A pdb=" N PHE A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 819 removed outlier: 3.659A pdb=" N ALA A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.678A pdb=" N GLN A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 856 removed outlier: 3.608A pdb=" N MET A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.595A pdb=" N ILE A 870 " --> pdb=" O ASN A 866 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 922 removed outlier: 3.755A pdb=" N SER A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 950 through 971 removed outlier: 3.802A pdb=" N ARG A 954 " --> pdb=" O SER A 950 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 994 removed outlier: 3.743A pdb=" N ALA A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1015 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.815A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1058 removed outlier: 3.622A pdb=" N ARG A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A1056 " --> pdb=" O ASP A1052 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A1058 " --> pdb=" O HIS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 4.278A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1110 removed outlier: 3.882A pdb=" N VAL A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1150 removed outlier: 3.824A pdb=" N LYS A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A1143 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A1144 " --> pdb=" O THR A1140 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1184 removed outlier: 4.300A pdb=" N ASP A1160 " --> pdb=" O GLY A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1191 through 1204 removed outlier: 3.570A pdb=" N LEU A1197 " --> pdb=" O ASN A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1219 removed outlier: 3.596A pdb=" N TYR A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A1215 " --> pdb=" O SER A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 removed outlier: 3.876A pdb=" N THR A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1271 Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.784A pdb=" N LEU A1294 " --> pdb=" O GLY A1291 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 238 removed outlier: 3.827A pdb=" N GLY B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.997A pdb=" N ILE B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.932A pdb=" N ASP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.121A pdb=" N SER B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 378 through 392 removed outlier: 3.610A pdb=" N LEU B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.162A pdb=" N LEU B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 448 through 465 Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 485 through 503 Processing helix chain 'B' and resid 503 through 509 removed outlier: 3.996A pdb=" N MET B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.870A pdb=" N VAL B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 520 Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.897A pdb=" N ARG B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 removed outlier: 4.135A pdb=" N ALA B 547 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 564 removed outlier: 3.877A pdb=" N LEU B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 560 " --> pdb=" O HIS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 586 removed outlier: 3.818A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.717A pdb=" N THR B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 642 removed outlier: 4.133A pdb=" N LEU B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 664 removed outlier: 3.571A pdb=" N PHE B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.552A pdb=" N VAL B 670 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 706 removed outlier: 4.316A pdb=" N LEU B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 729 through 745 removed outlier: 3.565A pdb=" N TYR B 733 " --> pdb=" O CYS B 729 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 800 removed outlier: 4.132A pdb=" N SER B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 800 " --> pdb=" O ILE B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 833 removed outlier: 4.342A pdb=" N GLU B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS B 828 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 829 " --> pdb=" O ILE B 825 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR B 833 " --> pdb=" O TYR B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.835A pdb=" N PHE B 925 " --> pdb=" O SER B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 938 removed outlier: 3.532A pdb=" N VAL B 932 " --> pdb=" O ASP B 929 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 937 " --> pdb=" O SER B 934 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 938 " --> pdb=" O ILE B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 980 removed outlier: 3.689A pdb=" N SER B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1019 removed outlier: 3.585A pdb=" N LEU B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1036 removed outlier: 4.009A pdb=" N ASN B1025 " --> pdb=" O THR B1021 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS B1026 " --> pdb=" O PRO B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1073 removed outlier: 3.709A pdb=" N SER B1060 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1082 Proline residue: B1081 - end of helix Processing helix chain 'B' and resid 1083 through 1097 removed outlier: 4.406A pdb=" N ARG B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1120 removed outlier: 3.539A pdb=" N LEU B1110 " --> pdb=" O PRO B1106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B1120 " --> pdb=" O HIS B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1124 removed outlier: 3.595A pdb=" N SER B1124 " --> pdb=" O PHE B1121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1121 through 1124' Processing helix chain 'B' and resid 1128 through 1143 removed outlier: 3.533A pdb=" N GLU B1143 " --> pdb=" O MET B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1165 removed outlier: 3.823A pdb=" N ALA B1156 " --> pdb=" O LYS B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1193 removed outlier: 3.501A pdb=" N HIS B1183 " --> pdb=" O ASN B1179 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B1184 " --> pdb=" O ASP B1180 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B1193 " --> pdb=" O TYR B1189 " (cutoff:3.500A) Processing helix chain 'B' and resid 1195 through 1213 removed outlier: 3.835A pdb=" N VAL B1208 " --> pdb=" O ALA B1204 " (cutoff:3.500A) Proline residue: B1209 - end of helix removed outlier: 3.845A pdb=" N ASN B1213 " --> pdb=" O PRO B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1248 removed outlier: 3.682A pdb=" N PHE B1234 " --> pdb=" O THR B1230 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B1248 " --> pdb=" O LYS B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1280 Processing helix chain 'B' and resid 1281 through 1283 No H-bonds generated for 'chain 'B' and resid 1281 through 1283' Processing helix chain 'B' and resid 1287 through 1310 removed outlier: 4.041A pdb=" N ARG B1299 " --> pdb=" O LEU B1295 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET B1310 " --> pdb=" O LEU B1306 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1316 removed outlier: 3.772A pdb=" N SER B1316 " --> pdb=" O LEU B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1348 removed outlier: 4.183A pdb=" N VAL B1324 " --> pdb=" O HIS B1320 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B1326 " --> pdb=" O GLU B1322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B1334 " --> pdb=" O THR B1330 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B1346 " --> pdb=" O CYS B1342 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B1348 " --> pdb=" O HIS B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1355 Processing helix chain 'B' and resid 1356 through 1378 removed outlier: 4.219A pdb=" N LEU B1367 " --> pdb=" O THR B1363 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B1368 " --> pdb=" O LEU B1364 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B1378 " --> pdb=" O MET B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1382 No H-bonds generated for 'chain 'B' and resid 1380 through 1382' Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.747A pdb=" N ASN C 60 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.531A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.513A pdb=" N GLY D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 143 Processing helix chain 'D' and resid 144 through 166 removed outlier: 4.152A pdb=" N GLN D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 199 through 225 removed outlier: 3.865A pdb=" N VAL D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.503A pdb=" N PHE D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 removed outlier: 3.718A pdb=" N PHE D 492 " --> pdb=" O ALA D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 744 removed outlier: 3.530A pdb=" N TYR D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 766 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 402 through 410 Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'E' and resid 531 through 534 removed outlier: 4.466A pdb=" N GLY E 534 " --> pdb=" O ARG E 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 531 through 534' Processing helix chain 'E' and resid 535 through 546 Processing helix chain 'E' and resid 547 through 555 removed outlier: 4.180A pdb=" N ILE E 553 " --> pdb=" O TRP E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 574 Processing helix chain 'E' and resid 592 through 605 removed outlier: 3.730A pdb=" N VAL E 596 " --> pdb=" O GLN E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 639 Processing helix chain 'E' and resid 653 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 8.331A pdb=" N LEU E 670 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR E 568 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR E 672 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN E 570 " --> pdb=" O TYR E 672 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 568 removed outlier: 3.704A pdb=" N VAL E 159 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.541A pdb=" N ASP A 570 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS E 109 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 103 " --> pdb=" O CYS E 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.943A pdb=" N SER A 659 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 4.045A pdb=" N TRP B1385 " --> pdb=" O LYS A1288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 681 through 683 Processing sheet with id=AA7, first strand: chain 'C' and resid 1 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.752A pdb=" N VAL C 70 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.741A pdb=" N GLY D 82 " --> pdb=" O THR D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 446 through 453 removed outlier: 6.540A pdb=" N GLN D 433 " --> pdb=" O ASP D 522 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 437 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 515 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.240A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 506 removed outlier: 3.510A pdb=" N CYS D 506 " --> pdb=" O HIS D 511 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 511 " --> pdb=" O CYS D 506 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 527 through 528 removed outlier: 3.655A pdb=" N SER D 575 " --> pdb=" O LEU D 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AB6, first strand: chain 'D' and resid 596 through 598 removed outlier: 7.162A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 421 through 423 removed outlier: 4.209A pdb=" N LEU E 429 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 20 " --> pdb=" O PRO E 514 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU E 519 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR E 524 " --> pdb=" O GLU E 519 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.674A pdb=" N ALA E 48 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU E 36 " --> pdb=" O PHE E 46 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE E 46 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU E 38 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 44 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 69 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER E 58 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR E 67 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 120 through 126 removed outlier: 4.353A pdb=" N ILE E 141 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER E 162 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 171 through 176 removed outlier: 7.241A pdb=" N LEU E 192 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS E 205 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL E 194 " --> pdb=" O LEU E 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 213 through 218 removed outlier: 3.923A pdb=" N ALA E 246 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER E 238 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS E 244 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 260 removed outlier: 4.225A pdb=" N GLY E 271 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 276 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 297 through 302 removed outlier: 6.724A pdb=" N ALA E 315 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET E 300 " --> pdb=" O TRP E 313 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP E 313 " --> pdb=" O MET E 300 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU E 302 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA E 311 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN E 322 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 355 " --> pdb=" O LYS E 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 363 through 368 removed outlier: 7.688A pdb=" N VAL E 384 " --> pdb=" O ASP E 397 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP E 397 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR E 386 " --> pdb=" O VAL E 395 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 442 through 444 1304 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7900 1.34 - 1.46: 5211 1.46 - 1.58: 12248 1.58 - 1.70: 114 1.70 - 1.82: 208 Bond restraints: 25681 Sorted by residual: bond pdb=" O5' DN T 50 " pdb=" P DN T 50 " ideal model delta sigma weight residual 1.720 1.596 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" O5' DN T 47 " pdb=" P DN T 47 " ideal model delta sigma weight residual 1.720 1.597 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O5' DN S 16 " pdb=" P DN S 16 " ideal model delta sigma weight residual 1.720 1.597 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O5' DN S 14 " pdb=" P DN S 14 " ideal model delta sigma weight residual 1.720 1.597 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O5' DN T 37 " pdb=" P DN T 37 " ideal model delta sigma weight residual 1.720 1.597 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 25676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 33982 2.83 - 5.67: 703 5.67 - 8.50: 130 8.50 - 11.34: 9 11.34 - 14.17: 1 Bond angle restraints: 34825 Sorted by residual: angle pdb=" N HIS E 73 " pdb=" CA HIS E 73 " pdb=" C HIS E 73 " ideal model delta sigma weight residual 110.80 121.58 -10.78 2.13e+00 2.20e-01 2.56e+01 angle pdb=" N GLU E 602 " pdb=" CA GLU E 602 " pdb=" C GLU E 602 " ideal model delta sigma weight residual 111.40 105.91 5.49 1.22e+00 6.72e-01 2.02e+01 angle pdb=" C GLU A1067 " pdb=" N LYS A1068 " pdb=" CA LYS A1068 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C GLU E 189 " pdb=" N LYS E 190 " pdb=" CA LYS E 190 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" CA LEU E 398 " pdb=" CB LEU E 398 " pdb=" CG LEU E 398 " ideal model delta sigma weight residual 116.30 130.47 -14.17 3.50e+00 8.16e-02 1.64e+01 ... (remaining 34820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 13936 18.08 - 36.16: 1778 36.16 - 54.25: 430 54.25 - 72.33: 95 72.33 - 90.41: 35 Dihedral angle restraints: 16274 sinusoidal: 7221 harmonic: 9053 Sorted by residual: dihedral pdb=" CA LEU A 641 " pdb=" C LEU A 641 " pdb=" N LEU A 642 " pdb=" CA LEU A 642 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN A 973 " pdb=" C GLN A 973 " pdb=" N GLU A 974 " pdb=" CA GLU A 974 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLY E 522 " pdb=" C GLY E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 16271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3463 0.067 - 0.133: 580 0.133 - 0.200: 45 0.200 - 0.266: 3 0.266 - 0.333: 2 Chirality restraints: 4093 Sorted by residual: chirality pdb=" CB ILE A 888 " pdb=" CA ILE A 888 " pdb=" CG1 ILE A 888 " pdb=" CG2 ILE A 888 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA HIS E 73 " pdb=" N HIS E 73 " pdb=" C HIS E 73 " pdb=" CB HIS E 73 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA THR B1021 " pdb=" N THR B1021 " pdb=" C THR B1021 " pdb=" CB THR B1021 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4090 not shown) Planarity restraints: 4243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 75 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C THR E 75 " -0.049 2.00e-02 2.50e+03 pdb=" O THR E 75 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 76 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 643 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 644 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 525 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO B 526 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.034 5.00e-02 4.00e+02 ... (remaining 4240 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4551 2.77 - 3.30: 24496 3.30 - 3.83: 39914 3.83 - 4.37: 43298 4.37 - 4.90: 76067 Nonbonded interactions: 188326 Sorted by model distance: nonbonded pdb=" ND2 ASN D 85 " pdb=" O GLY D 87 " model vdw 2.236 3.120 nonbonded pdb=" NE2 HIS B 550 " pdb=" OG SER D 772 " model vdw 2.264 3.120 nonbonded pdb=" OE1 GLU D 442 " pdb=" OG1 THR D 513 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU C 16 " pdb=" OH TYR D 512 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP A 728 " pdb=" OG SER A 730 " model vdw 2.284 3.040 ... (remaining 188321 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 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.860 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.008 0.127 25687 Z= 0.408 Angle : 0.958 14.171 34833 Z= 0.468 Chirality : 0.049 0.333 4093 Planarity : 0.005 0.071 4243 Dihedral : 17.354 90.408 10349 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.15), residues: 3018 helix: 0.34 (0.13), residues: 1612 sheet: -0.46 (0.32), residues: 252 loop : -1.63 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1392 TYR 0.025 0.002 TYR E 386 PHE 0.040 0.002 PHE E 567 TRP 0.037 0.003 TRP A 375 HIS 0.009 0.001 HIS E 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.40 (25681) covalent geometry : angle 0.95625 / 0.47 (34825) SS BOND : bond 0.00321 / 0.17 ( 1) SS BOND : angle 1.57047 / 0.88 ( 2) hydrogen bonds : bond 0.15570 / 10.77 ( 1304) hydrogen bonds : angle 5.62924 / 3.99 ( 3762) metal coordination : bond 0.07206 / 3.60 ( 4) metal coordination : angle 4.25892 / 2.35 ( 6) Misc. bond : bond 0.12729 / 6.70 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8660 (tp-100) REVERT: A 413 MET cc_start: 0.7983 (tpt) cc_final: 0.7758 (tpp) REVERT: A 486 ASP cc_start: 0.7976 (m-30) cc_final: 0.7767 (m-30) REVERT: A 587 ILE cc_start: 0.9388 (tt) cc_final: 0.9143 (tt) REVERT: A 624 MET cc_start: 0.7979 (tpp) cc_final: 0.7649 (mmm) REVERT: A 725 LYS cc_start: 0.7633 (pptt) cc_final: 0.7003 (tppt) REVERT: A 909 LEU cc_start: 0.8609 (tp) cc_final: 0.8332 (tp) REVERT: A 1093 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 1127 ASN cc_start: 0.7455 (m-40) cc_final: 0.7019 (m-40) REVERT: B 523 ASN cc_start: 0.7673 (t0) cc_final: 0.7223 (t0) REVERT: B 782 MET cc_start: 0.8048 (ttm) cc_final: 0.7616 (tpt) REVERT: B 1216 LYS cc_start: 0.9112 (tptt) cc_final: 0.8801 (tptm) REVERT: B 1270 MET cc_start: 0.8080 (mtt) cc_final: 0.7859 (mtm) REVERT: D 172 ASP cc_start: 0.8471 (p0) cc_final: 0.7989 (p0) REVERT: E 569 LEU cc_start: 0.8538 (mm) cc_final: 0.8334 (mt) REVERT: E 603 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7311 (tmtt) REVERT: E 670 LEU cc_start: 0.9022 (mt) cc_final: 0.8816 (mp) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.1628 time to fit residues: 135.8431 Evaluate side-chains 307 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.0020 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN A 621 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B1063 GLN B1308 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN D 114 ASN D 531 HIS ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094645 restraints weight = 47023.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097330 restraints weight = 25431.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099087 restraints weight = 16956.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.100334 restraints weight = 12932.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101091 restraints weight = 10793.701| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25687 Z= 0.125 Angle : 0.704 11.038 34833 Z= 0.338 Chirality : 0.041 0.216 4093 Planarity : 0.004 0.073 4243 Dihedral : 8.855 58.017 4286 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.56 % Allowed : 15.71 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.15), residues: 3018 helix: 0.97 (0.13), residues: 1643 sheet: 0.12 (0.33), residues: 245 loop : -1.44 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 932 TYR 0.018 0.001 TYR A 359 PHE 0.015 0.001 PHE A 202 TRP 0.032 0.002 TRP E 102 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (25681) covalent geometry : angle 0.70236 / 0.34 (34825) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 0.98477 / 0.52 ( 2) hydrogen bonds : bond 0.04074 / 2.78 ( 1304) hydrogen bonds : angle 4.26218 / 3.03 ( 3762) metal coordination : bond 0.00398 / 0.20 ( 4) metal coordination : angle 3.57941 / 2.60 ( 6) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8907 (tp-100) REVERT: A 525 MET cc_start: 0.8976 (tpp) cc_final: 0.8659 (ttp) REVERT: A 581 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7936 (tt0) REVERT: A 624 MET cc_start: 0.8264 (tpp) cc_final: 0.8006 (mmm) REVERT: A 725 LYS cc_start: 0.7454 (pptt) cc_final: 0.6761 (mmmt) REVERT: A 909 LEU cc_start: 0.8815 (tp) cc_final: 0.8449 (tp) REVERT: A 1093 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 304 LYS cc_start: 0.8856 (tptm) cc_final: 0.8391 (tppt) REVERT: B 380 PHE cc_start: 0.7991 (t80) cc_final: 0.7602 (t80) REVERT: B 507 MET cc_start: 0.9186 (tpp) cc_final: 0.8948 (tpp) REVERT: B 523 ASN cc_start: 0.7726 (t0) cc_final: 0.7167 (t0) REVERT: B 581 MET cc_start: 0.8562 (ttm) cc_final: 0.8317 (ttm) REVERT: B 782 MET cc_start: 0.8022 (ttm) cc_final: 0.7476 (tpt) REVERT: B 800 PHE cc_start: 0.8353 (m-80) cc_final: 0.8023 (m-80) REVERT: B 808 MET cc_start: 0.7577 (tpt) cc_final: 0.6806 (tpt) REVERT: B 1099 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8478 (tptp) REVERT: B 1307 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8535 (ttpt) REVERT: B 1364 LEU cc_start: 0.9257 (tp) cc_final: 0.8985 (tt) REVERT: C 2 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 41 GLN cc_start: 0.8921 (mp10) cc_final: 0.8598 (mp10) REVERT: C 60 ASN cc_start: 0.8637 (t0) cc_final: 0.8364 (t0) REVERT: D 110 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7845 (mtmt) REVERT: D 172 ASP cc_start: 0.8371 (p0) cc_final: 0.7903 (p0) REVERT: E 204 MET cc_start: 0.8794 (ppp) cc_final: 0.7361 (ppp) REVERT: E 443 VAL cc_start: 0.8476 (t) cc_final: 0.8227 (t) REVERT: E 594 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7618 (mtp85) REVERT: E 603 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7510 (tmtt) outliers start: 44 outliers final: 23 residues processed: 390 average time/residue: 0.1459 time to fit residues: 93.5642 Evaluate side-chains 319 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1307 LYS Chi-restraints excluded: chain B residue 1308 GLN Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [279, 188, 191, 69, 75, 261, 165, 240, 208, 158, 91] chunk 279 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN B 545 ASN B 637 ASN C 25 ASN C 62 GLN D 85 ASN D 205 GLN ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090786 restraints weight = 47843.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093378 restraints weight = 26024.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095119 restraints weight = 17463.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096263 restraints weight = 13404.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097006 restraints weight = 11228.893| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25687 Z= 0.153 Angle : 0.672 11.109 34833 Z= 0.325 Chirality : 0.041 0.196 4093 Planarity : 0.004 0.079 4243 Dihedral : 8.570 59.795 4286 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.77 % Allowed : 18.77 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.16), residues: 3018 helix: 1.14 (0.13), residues: 1651 sheet: 0.10 (0.33), residues: 255 loop : -1.37 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 447 TYR 0.040 0.001 TYR A 359 PHE 0.028 0.001 PHE A 459 TRP 0.025 0.002 TRP E 102 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (25681) covalent geometry : angle 0.67015 / 0.33 (34825) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 1.33900 / 0.75 ( 2) hydrogen bonds : bond 0.04103 / 2.77 ( 1304) hydrogen bonds : angle 4.17120 / 2.99 ( 3762) metal coordination : bond 0.00354 / 0.17 ( 4) metal coordination : angle 3.31213 / 2.04 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 304 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8921 (tp-100) REVERT: A 525 MET cc_start: 0.8972 (tpp) cc_final: 0.8686 (ttp) REVERT: A 581 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8075 (tt0) REVERT: A 624 MET cc_start: 0.8302 (tpp) cc_final: 0.8010 (mmm) REVERT: A 725 LYS cc_start: 0.7485 (pptt) cc_final: 0.6812 (mmmt) REVERT: A 1093 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 246 LEU cc_start: 0.8934 (mm) cc_final: 0.8685 (mm) REVERT: B 361 SER cc_start: 0.8786 (p) cc_final: 0.8509 (p) REVERT: B 380 PHE cc_start: 0.8125 (t80) cc_final: 0.7782 (t80) REVERT: B 485 ASN cc_start: 0.7288 (t0) cc_final: 0.5840 (t0) REVERT: B 523 ASN cc_start: 0.7689 (t0) cc_final: 0.7145 (t0) REVERT: B 581 MET cc_start: 0.8610 (ttm) cc_final: 0.8396 (ttm) REVERT: B 782 MET cc_start: 0.8006 (ttm) cc_final: 0.7493 (tpt) REVERT: B 800 PHE cc_start: 0.8490 (m-80) cc_final: 0.8188 (m-80) REVERT: B 1063 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: B 1099 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8448 (tptp) REVERT: C 41 GLN cc_start: 0.8896 (mp10) cc_final: 0.8505 (mp10) REVERT: C 60 ASN cc_start: 0.8732 (t0) cc_final: 0.8350 (t0) REVERT: D 110 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8086 (mtpt) REVERT: D 172 ASP cc_start: 0.8346 (p0) cc_final: 0.7856 (p0) REVERT: D 210 ASN cc_start: 0.7792 (t0) cc_final: 0.7571 (t0) REVERT: D 502 ASP cc_start: 0.8175 (m-30) cc_final: 0.7956 (m-30) REVERT: E 118 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: E 603 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7484 (tmtt) outliers start: 78 outliers final: 43 residues processed: 360 average time/residue: 0.1340 time to fit residues: 81.4931 Evaluate side-chains 313 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1359 LEU Chi-restraints excluded: chain B residue 1371 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 501 GLN Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [108, 157, 153, 79, 201, 190, 301, 114, 106, 80, 118] chunk 108 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 301 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 212 GLN E 167 ASN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091516 restraints weight = 47057.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094052 restraints weight = 25944.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095784 restraints weight = 17566.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096938 restraints weight = 13476.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097635 restraints weight = 11323.092| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25687 Z= 0.136 Angle : 0.654 11.448 34833 Z= 0.315 Chirality : 0.040 0.191 4093 Planarity : 0.004 0.081 4243 Dihedral : 8.341 59.950 4286 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 21.19 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.16), residues: 3018 helix: 1.23 (0.13), residues: 1655 sheet: 0.03 (0.33), residues: 245 loop : -1.34 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.034 0.001 TYR A 359 PHE 0.027 0.001 PHE B 380 TRP 0.023 0.002 TRP A 375 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25681) covalent geometry : angle 0.65303 / 0.32 (34825) SS BOND : bond 0.01684 / 0.89 ( 1) SS BOND : angle 1.36602 / 0.75 ( 2) hydrogen bonds : bond 0.03883 / 2.63 ( 1304) hydrogen bonds : angle 4.04151 / 2.90 ( 3762) metal coordination : bond 0.00243 / 0.12 ( 4) metal coordination : angle 2.97873 / 1.92 ( 6) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 294 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8845 (tp-100) REVERT: A 254 LEU cc_start: 0.8541 (pt) cc_final: 0.8311 (pp) REVERT: A 525 MET cc_start: 0.8946 (tpp) cc_final: 0.8676 (ttp) REVERT: A 588 MET cc_start: 0.7632 (tmm) cc_final: 0.7405 (tmm) REVERT: A 600 ASP cc_start: 0.7357 (p0) cc_final: 0.6938 (p0) REVERT: A 624 MET cc_start: 0.8311 (tpp) cc_final: 0.7998 (mmm) REVERT: A 725 LYS cc_start: 0.7509 (pptt) cc_final: 0.6799 (mmmt) REVERT: A 1093 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 1166 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 246 LEU cc_start: 0.8956 (mm) cc_final: 0.8751 (mm) REVERT: B 485 ASN cc_start: 0.7355 (t0) cc_final: 0.6670 (t0) REVERT: B 523 ASN cc_start: 0.7643 (t0) cc_final: 0.7142 (t0) REVERT: B 581 MET cc_start: 0.8671 (ttm) cc_final: 0.8454 (ttm) REVERT: B 782 MET cc_start: 0.7988 (ttm) cc_final: 0.7490 (tpt) REVERT: B 800 PHE cc_start: 0.8457 (m-80) cc_final: 0.8150 (m-80) REVERT: B 1058 MET cc_start: 0.8007 (mmm) cc_final: 0.7748 (mmt) REVERT: B 1099 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8450 (tptp) REVERT: C 41 GLN cc_start: 0.8900 (mp10) cc_final: 0.8608 (mp10) REVERT: C 60 ASN cc_start: 0.8765 (t0) cc_final: 0.8348 (t0) REVERT: D 172 ASP cc_start: 0.8280 (p0) cc_final: 0.7815 (p0) REVERT: D 210 ASN cc_start: 0.7802 (t0) cc_final: 0.7591 (t0) REVERT: E 118 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: E 413 MET cc_start: 0.7748 (tpt) cc_final: 0.7457 (tpt) REVERT: E 603 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7476 (tmtt) outliers start: 78 outliers final: 50 residues processed: 354 average time/residue: 0.1349 time to fit residues: 80.6269 Evaluate side-chains 329 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [110, 226, 194, 199, 32, 113, 276, 162, 13, 58, 15] chunk 110 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 276 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093324 restraints weight = 46791.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095954 restraints weight = 25418.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097692 restraints weight = 16998.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098829 restraints weight = 13013.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099592 restraints weight = 10878.519| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25687 Z= 0.114 Angle : 0.633 10.459 34833 Z= 0.303 Chirality : 0.040 0.191 4093 Planarity : 0.004 0.083 4243 Dihedral : 8.087 59.810 4286 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.88 % Allowed : 21.61 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 3018 helix: 1.34 (0.13), residues: 1656 sheet: -0.01 (0.32), residues: 260 loop : -1.34 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 779 TYR 0.022 0.001 TYR A 359 PHE 0.016 0.001 PHE A 459 TRP 0.022 0.001 TRP E 102 HIS 0.006 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (25681) covalent geometry : angle 0.63254 / 0.30 (34825) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 1.24014 / 0.69 ( 2) hydrogen bonds : bond 0.03557 / 2.39 ( 1304) hydrogen bonds : angle 3.89083 / 2.80 ( 3762) metal coordination : bond 0.00158 / 0.08 ( 4) metal coordination : angle 2.55160 / 1.70 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9293 (mm-40) cc_final: 0.8844 (tp-100) REVERT: A 525 MET cc_start: 0.8939 (tpp) cc_final: 0.8681 (ttp) REVERT: A 534 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8278 (mmmm) REVERT: A 588 MET cc_start: 0.7593 (tmm) cc_final: 0.7299 (tmm) REVERT: A 591 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8811 (mp) REVERT: A 624 MET cc_start: 0.8281 (tpp) cc_final: 0.7969 (mmm) REVERT: A 725 LYS cc_start: 0.7433 (pptt) cc_final: 0.6772 (mmmt) REVERT: A 970 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 1093 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 1166 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 246 LEU cc_start: 0.8954 (mm) cc_final: 0.8739 (mm) REVERT: B 270 LEU cc_start: 0.8692 (tp) cc_final: 0.8327 (tp) REVERT: B 304 LYS cc_start: 0.8851 (tptm) cc_final: 0.8369 (tppt) REVERT: B 523 ASN cc_start: 0.7674 (t0) cc_final: 0.7183 (t0) REVERT: B 581 MET cc_start: 0.8640 (ttm) cc_final: 0.8401 (ttm) REVERT: B 782 MET cc_start: 0.7974 (ttm) cc_final: 0.7480 (tpt) REVERT: B 800 PHE cc_start: 0.8390 (m-80) cc_final: 0.8100 (m-80) REVERT: B 1058 MET cc_start: 0.8029 (mmm) cc_final: 0.7780 (mmt) REVERT: B 1099 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8443 (tptp) REVERT: C 41 GLN cc_start: 0.8916 (mp10) cc_final: 0.8589 (mp10) REVERT: C 60 ASN cc_start: 0.8785 (t0) cc_final: 0.8357 (t0) REVERT: D 110 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8052 (mtpt) REVERT: D 172 ASP cc_start: 0.8293 (p0) cc_final: 0.7822 (p0) REVERT: D 210 ASN cc_start: 0.7796 (t0) cc_final: 0.7575 (t0) REVERT: E 118 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7622 (m-30) outliers start: 81 outliers final: 50 residues processed: 363 average time/residue: 0.1338 time to fit residues: 81.3588 Evaluate side-chains 333 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1170 TYR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [303, 215, 161, 34, 83, 218, 199, 270, 123, 59, 107] chunk 303 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN ** B 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN C 62 GLN D 205 GLN E 167 ASN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087641 restraints weight = 47117.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090077 restraints weight = 26248.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091732 restraints weight = 17849.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092826 restraints weight = 13848.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093345 restraints weight = 11649.527| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25687 Z= 0.231 Angle : 0.725 11.838 34833 Z= 0.354 Chirality : 0.043 0.185 4093 Planarity : 0.004 0.088 4243 Dihedral : 8.155 59.439 4286 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.02 % Allowed : 22.43 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.16), residues: 3018 helix: 1.21 (0.13), residues: 1656 sheet: -0.21 (0.32), residues: 271 loop : -1.43 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1285 TYR 0.025 0.002 TYR A 359 PHE 0.021 0.002 PHE B1305 TRP 0.034 0.002 TRP A 375 HIS 0.007 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (25681) covalent geometry : angle 0.72337 / 0.35 (34825) SS BOND : bond 0.00467 / 0.25 ( 1) SS BOND : angle 1.54416 / 0.88 ( 2) hydrogen bonds : bond 0.04638 / 3.14 ( 1304) hydrogen bonds : angle 4.26932 / 3.06 ( 3762) metal coordination : bond 0.00608 / 0.30 ( 4) metal coordination : angle 3.63513 / 2.03 ( 6) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 271 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8897 (tp-100) REVERT: A 384 GLU cc_start: 0.8352 (tp30) cc_final: 0.8084 (tp30) REVERT: A 525 MET cc_start: 0.8985 (tpp) cc_final: 0.8736 (ttp) REVERT: A 534 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (mmmm) REVERT: A 588 MET cc_start: 0.7772 (tmm) cc_final: 0.7412 (tmm) REVERT: A 591 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 624 MET cc_start: 0.8367 (tpp) cc_final: 0.8042 (mmm) REVERT: A 725 LYS cc_start: 0.7648 (pptt) cc_final: 0.7081 (tppt) REVERT: A 1093 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 1166 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8633 (tt) REVERT: B 209 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7842 (m90) REVERT: B 485 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7000 (t0) REVERT: B 523 ASN cc_start: 0.7657 (t0) cc_final: 0.7141 (t0) REVERT: B 581 MET cc_start: 0.8731 (ttm) cc_final: 0.8410 (ttt) REVERT: B 738 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8506 (ttp-170) REVERT: B 782 MET cc_start: 0.8007 (ttm) cc_final: 0.7498 (tpt) REVERT: B 800 PHE cc_start: 0.8613 (m-80) cc_final: 0.8330 (m-80) REVERT: B 808 MET cc_start: 0.6753 (mmt) cc_final: 0.6535 (tpt) REVERT: C 41 GLN cc_start: 0.8898 (mp10) cc_final: 0.8512 (mp10) REVERT: C 60 ASN cc_start: 0.8875 (t0) cc_final: 0.8491 (t0) REVERT: D 172 ASP cc_start: 0.8313 (p0) cc_final: 0.7786 (p0) REVERT: E 117 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8605 (mtmm) outliers start: 113 outliers final: 72 residues processed: 358 average time/residue: 0.1444 time to fit residues: 86.4463 Evaluate side-chains 339 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 261 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1359 LEU Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [34, 192, 189, 149, 4, 83, 53, 81, 145, 210, 99] chunk 34 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B 523 ASN D 198 HIS D 205 GLN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093968 restraints weight = 49332.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096819 restraints weight = 25530.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098729 restraints weight = 16798.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099923 restraints weight = 12786.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100726 restraints weight = 10729.126| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25687 Z= 0.142 Angle : 0.670 12.762 34833 Z= 0.321 Chirality : 0.041 0.186 4093 Planarity : 0.004 0.089 4243 Dihedral : 7.991 59.345 4286 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.59 % Allowed : 23.36 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.16), residues: 3018 helix: 1.36 (0.13), residues: 1657 sheet: -0.32 (0.32), residues: 274 loop : -1.40 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1097 TYR 0.026 0.001 TYR A 283 PHE 0.015 0.001 PHE B1305 TRP 0.036 0.002 TRP B 651 HIS 0.007 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (25681) covalent geometry : angle 0.66922 / 0.32 (34825) SS BOND : bond 0.00428 / 0.23 ( 1) SS BOND : angle 1.52274 / 0.86 ( 2) hydrogen bonds : bond 0.03956 / 2.67 ( 1304) hydrogen bonds : angle 3.99241 / 2.87 ( 3762) metal coordination : bond 0.00333 / 0.16 ( 4) metal coordination : angle 2.94663 / 1.86 ( 6) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 281 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9447 (mm-40) cc_final: 0.8965 (tp-100) REVERT: A 384 GLU cc_start: 0.8577 (tp30) cc_final: 0.8215 (tp30) REVERT: A 525 MET cc_start: 0.9097 (tpp) cc_final: 0.8822 (ttp) REVERT: A 534 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8362 (mmmm) REVERT: A 588 MET cc_start: 0.7676 (tmm) cc_final: 0.7289 (tmm) REVERT: A 591 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 624 MET cc_start: 0.8403 (tpp) cc_final: 0.8055 (mmm) REVERT: A 725 LYS cc_start: 0.7684 (pptt) cc_final: 0.6926 (mmmt) REVERT: A 1093 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 1166 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 1203 SER cc_start: 0.8356 (t) cc_final: 0.8077 (p) REVERT: A 1273 VAL cc_start: 0.6595 (OUTLIER) cc_final: 0.6270 (p) REVERT: B 209 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7937 (m90) REVERT: B 523 ASN cc_start: 0.7723 (t0) cc_final: 0.7236 (t0) REVERT: B 581 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8504 (ttt) REVERT: B 782 MET cc_start: 0.8120 (ttm) cc_final: 0.7466 (tpt) REVERT: B 800 PHE cc_start: 0.8596 (m-80) cc_final: 0.8320 (m-80) REVERT: B 1058 MET cc_start: 0.8216 (mmm) cc_final: 0.7994 (mmt) REVERT: C 41 GLN cc_start: 0.8964 (mp10) cc_final: 0.8520 (mp10) REVERT: C 60 ASN cc_start: 0.8947 (t0) cc_final: 0.8539 (t0) REVERT: D 97 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8598 (mm110) REVERT: D 172 ASP cc_start: 0.8397 (p0) cc_final: 0.7842 (p0) REVERT: D 192 TYR cc_start: 0.8047 (m-10) cc_final: 0.7527 (m-10) REVERT: D 210 ASN cc_start: 0.7959 (t0) cc_final: 0.7695 (t0) REVERT: E 413 MET cc_start: 0.8069 (tpt) cc_final: 0.7753 (tpt) outliers start: 101 outliers final: 74 residues processed: 358 average time/residue: 0.1396 time to fit residues: 83.4835 Evaluate side-chains 349 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 269 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1170 TYR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [167, 272, 206, 107, 277, 134, 21, 150, 116, 289, 67] chunk 167 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093305 restraints weight = 50400.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096172 restraints weight = 26233.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098061 restraints weight = 17256.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099274 restraints weight = 13161.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100061 restraints weight = 11014.406| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25687 Z= 0.173 Angle : 0.696 12.995 34833 Z= 0.333 Chirality : 0.042 0.184 4093 Planarity : 0.004 0.092 4243 Dihedral : 7.955 58.771 4286 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.66 % Allowed : 24.07 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 3018 helix: 1.35 (0.13), residues: 1656 sheet: -0.27 (0.33), residues: 254 loop : -1.44 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1285 TYR 0.030 0.002 TYR A 283 PHE 0.016 0.001 PHE B1305 TRP 0.036 0.002 TRP B 651 HIS 0.007 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (25681) covalent geometry : angle 0.69463 / 0.33 (34825) SS BOND : bond 0.00419 / 0.22 ( 1) SS BOND : angle 1.52808 / 0.87 ( 2) hydrogen bonds : bond 0.04109 / 2.77 ( 1304) hydrogen bonds : angle 4.05204 / 2.91 ( 3762) metal coordination : bond 0.00439 / 0.22 ( 4) metal coordination : angle 3.16453 / 1.93 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 269 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9498 (mm-40) cc_final: 0.8928 (tp-100) REVERT: A 384 GLU cc_start: 0.8605 (tp30) cc_final: 0.8281 (tp30) REVERT: A 525 MET cc_start: 0.9084 (tpp) cc_final: 0.8839 (ttp) REVERT: A 534 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8310 (mmmm) REVERT: A 588 MET cc_start: 0.7730 (tmm) cc_final: 0.7293 (tmm) REVERT: A 591 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 600 ASP cc_start: 0.7503 (p0) cc_final: 0.7224 (p0) REVERT: A 624 MET cc_start: 0.8435 (tpp) cc_final: 0.8089 (mmm) REVERT: A 725 LYS cc_start: 0.7716 (pptt) cc_final: 0.7272 (tppt) REVERT: A 781 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 1093 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 1166 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 1203 SER cc_start: 0.8361 (t) cc_final: 0.8061 (p) REVERT: A 1273 VAL cc_start: 0.6490 (OUTLIER) cc_final: 0.6146 (p) REVERT: B 209 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7976 (m90) REVERT: B 523 ASN cc_start: 0.7705 (t0) cc_final: 0.7222 (t0) REVERT: B 581 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: B 782 MET cc_start: 0.8135 (ttm) cc_final: 0.7493 (tpt) REVERT: B 800 PHE cc_start: 0.8655 (m-80) cc_final: 0.8377 (m-80) REVERT: B 808 MET cc_start: 0.6843 (mmt) cc_final: 0.6607 (mmt) REVERT: B 1058 MET cc_start: 0.8224 (mmm) cc_final: 0.7928 (mmt) REVERT: B 1097 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5311 (mtm-85) REVERT: C 41 GLN cc_start: 0.8968 (mp10) cc_final: 0.8489 (mp10) REVERT: C 60 ASN cc_start: 0.8968 (t0) cc_final: 0.8571 (t0) REVERT: D 172 ASP cc_start: 0.8403 (p0) cc_final: 0.7848 (p0) REVERT: D 192 TYR cc_start: 0.7982 (m-10) cc_final: 0.7399 (m-10) REVERT: E 413 MET cc_start: 0.8072 (tpt) cc_final: 0.7766 (tpt) outliers start: 103 outliers final: 76 residues processed: 351 average time/residue: 0.1349 time to fit residues: 79.8675 Evaluate side-chains 350 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 266 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1097 ARG Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain B residue 1371 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [245, 305, 95, 197, 42, 104, 212, 195, 250, 284, 7] chunk 245 optimal weight: 0.1980 chunk 305 optimal weight: 0.7980 chunk 95 optimal weight: 0.0870 chunk 197 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097198 restraints weight = 49497.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100147 restraints weight = 25432.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102045 restraints weight = 16587.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103351 restraints weight = 12590.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104154 restraints weight = 10471.719| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25687 Z= 0.113 Angle : 0.673 13.648 34833 Z= 0.317 Chirality : 0.040 0.185 4093 Planarity : 0.004 0.092 4243 Dihedral : 7.724 59.142 4286 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.56 % Allowed : 25.24 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.16), residues: 3018 helix: 1.51 (0.13), residues: 1663 sheet: -0.10 (0.33), residues: 265 loop : -1.38 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1285 TYR 0.026 0.001 TYR A 283 PHE 0.012 0.001 PHE A 237 TRP 0.041 0.001 TRP B 651 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (25681) covalent geometry : angle 0.67168 / 0.32 (34825) SS BOND : bond 0.00594 / 0.31 ( 1) SS BOND : angle 1.56670 / 0.87 ( 2) hydrogen bonds : bond 0.03387 / 2.27 ( 1304) hydrogen bonds : angle 3.78707 / 2.73 ( 3762) metal coordination : bond 0.00177 / 0.09 ( 4) metal coordination : angle 2.81673 / 2.06 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9045 (pmm) cc_final: 0.8823 (pmm) REVERT: A 216 GLN cc_start: 0.9467 (mm-40) cc_final: 0.8899 (tp-100) REVERT: A 525 MET cc_start: 0.9033 (tpp) cc_final: 0.8808 (ttp) REVERT: A 534 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8233 (mmmm) REVERT: A 588 MET cc_start: 0.7545 (tmm) cc_final: 0.7218 (tmm) REVERT: A 591 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 600 ASP cc_start: 0.7264 (p0) cc_final: 0.6955 (p0) REVERT: A 624 MET cc_start: 0.8345 (tpp) cc_final: 0.8011 (mmm) REVERT: A 725 LYS cc_start: 0.7661 (pptt) cc_final: 0.7145 (mmmt) REVERT: A 841 TYR cc_start: 0.8572 (t80) cc_final: 0.8261 (t80) REVERT: A 1093 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 1166 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8494 (tt) REVERT: A 1203 SER cc_start: 0.8338 (t) cc_final: 0.8110 (p) REVERT: B 209 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7938 (m90) REVERT: B 523 ASN cc_start: 0.7629 (t0) cc_final: 0.7214 (t0) REVERT: B 581 MET cc_start: 0.8783 (ttm) cc_final: 0.8449 (ttt) REVERT: B 782 MET cc_start: 0.8096 (ttm) cc_final: 0.7496 (tpt) REVERT: B 800 PHE cc_start: 0.8488 (m-80) cc_final: 0.8244 (m-80) REVERT: B 808 MET cc_start: 0.6939 (mmt) cc_final: 0.6712 (mmt) REVERT: B 1139 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7798 (mmm) REVERT: C 41 GLN cc_start: 0.8986 (mp10) cc_final: 0.8509 (mp10) REVERT: C 60 ASN cc_start: 0.8947 (t0) cc_final: 0.8618 (t0) REVERT: D 97 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8459 (mm110) REVERT: D 110 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8172 (mtpt) REVERT: D 172 ASP cc_start: 0.8415 (p0) cc_final: 0.7838 (p0) REVERT: D 192 TYR cc_start: 0.7656 (m-10) cc_final: 0.6971 (m-10) REVERT: D 210 ASN cc_start: 0.7823 (t0) cc_final: 0.7584 (t0) REVERT: E 413 MET cc_start: 0.8051 (tpt) cc_final: 0.7751 (tpt) REVERT: E 569 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8252 (mp) outliers start: 72 outliers final: 51 residues processed: 360 average time/residue: 0.1343 time to fit residues: 81.5916 Evaluate side-chains 340 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1170 TYR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [169, 13, 249, 229, 265, 78, 264, 244, 60, 154, 205] chunk 169 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097213 restraints weight = 49667.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100162 restraints weight = 25744.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102130 restraints weight = 16889.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103404 restraints weight = 12812.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104168 restraints weight = 10682.711| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25687 Z= 0.120 Angle : 0.678 13.462 34833 Z= 0.320 Chirality : 0.040 0.186 4093 Planarity : 0.004 0.094 4243 Dihedral : 7.616 58.876 4286 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.38 % Allowed : 25.49 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.16), residues: 3018 helix: 1.56 (0.13), residues: 1656 sheet: -0.11 (0.33), residues: 265 loop : -1.39 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1285 TYR 0.040 0.001 TYR A 283 PHE 0.012 0.001 PHE B 541 TRP 0.032 0.001 TRP B 651 HIS 0.005 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (25681) covalent geometry : angle 0.67638 / 0.32 (34825) SS BOND : bond 0.00368 / 0.19 ( 1) SS BOND : angle 1.52002 / 0.85 ( 2) hydrogen bonds : bond 0.03458 / 2.32 ( 1304) hydrogen bonds : angle 3.79097 / 2.74 ( 3762) metal coordination : bond 0.00252 / 0.12 ( 4) metal coordination : angle 2.97373 / 2.10 ( 6) Misc. bond : bond 0.00020 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9489 (mm-40) cc_final: 0.8918 (tp-100) REVERT: A 384 GLU cc_start: 0.8590 (tp30) cc_final: 0.8337 (tp30) REVERT: A 485 PHE cc_start: 0.9177 (m-80) cc_final: 0.8826 (m-10) REVERT: A 525 MET cc_start: 0.9053 (tpp) cc_final: 0.8837 (ttp) REVERT: A 534 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8164 (mmmm) REVERT: A 588 MET cc_start: 0.7599 (tmm) cc_final: 0.7267 (tmm) REVERT: A 591 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8651 (mp) REVERT: A 600 ASP cc_start: 0.7300 (p0) cc_final: 0.7063 (p0) REVERT: A 624 MET cc_start: 0.8290 (tpp) cc_final: 0.7947 (mmm) REVERT: A 725 LYS cc_start: 0.7952 (pptt) cc_final: 0.7223 (mmmt) REVERT: A 1093 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 1166 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (tt) REVERT: A 1203 SER cc_start: 0.8402 (t) cc_final: 0.8096 (p) REVERT: B 209 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.7971 (m90) REVERT: B 523 ASN cc_start: 0.7606 (t0) cc_final: 0.7223 (t0) REVERT: B 581 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8535 (ttm) REVERT: B 782 MET cc_start: 0.8129 (ttm) cc_final: 0.7469 (tpt) REVERT: B 800 PHE cc_start: 0.8504 (m-80) cc_final: 0.8285 (m-80) REVERT: B 808 MET cc_start: 0.6974 (mmt) cc_final: 0.6671 (mmt) REVERT: B 1139 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: C 41 GLN cc_start: 0.9013 (mp10) cc_final: 0.8552 (mp10) REVERT: C 60 ASN cc_start: 0.8941 (t0) cc_final: 0.8644 (t0) REVERT: D 97 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8317 (mm110) REVERT: D 110 LYS cc_start: 0.8543 (tmtt) cc_final: 0.8178 (mtpt) REVERT: D 143 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.5179 (t80) REVERT: D 172 ASP cc_start: 0.8427 (p0) cc_final: 0.7906 (p0) REVERT: D 192 TYR cc_start: 0.7664 (m-10) cc_final: 0.6965 (m-10) REVERT: D 210 ASN cc_start: 0.7990 (t0) cc_final: 0.7776 (t0) REVERT: E 413 MET cc_start: 0.8073 (tpt) cc_final: 0.7757 (tpt) REVERT: E 569 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8253 (mp) REVERT: E 673 ARG cc_start: 0.6353 (ptp-170) cc_final: 0.5697 (ptp-170) outliers start: 67 outliers final: 54 residues processed: 336 average time/residue: 0.1333 time to fit residues: 75.7554 Evaluate side-chains 342 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 280 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1170 TYR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1364 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [135, 84, 197, 21, 95, 111, 67, 35, 15, 213, 276] chunk 135 optimal weight: 4.9990 chunk 84 optimal weight: 0.0570 chunk 197 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 276 optimal weight: 0.4980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098047 restraints weight = 49346.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101007 restraints weight = 25551.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102976 restraints weight = 16744.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104254 restraints weight = 12673.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105072 restraints weight = 10567.416| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25687 Z= 0.115 Angle : 0.685 17.458 34833 Z= 0.321 Chirality : 0.040 0.185 4093 Planarity : 0.004 0.094 4243 Dihedral : 7.493 59.103 4286 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 25.70 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.16), residues: 3018 helix: 1.62 (0.13), residues: 1654 sheet: -0.09 (0.33), residues: 267 loop : -1.35 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1285 TYR 0.035 0.001 TYR A 283 PHE 0.015 0.001 PHE B 541 TRP 0.034 0.001 TRP B 651 HIS 0.005 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (25681) covalent geometry : angle 0.68344 / 0.32 (34825) SS BOND : bond 0.00367 / 0.19 ( 1) SS BOND : angle 1.49096 / 0.84 ( 2) hydrogen bonds : bond 0.03365 / 2.26 ( 1304) hydrogen bonds : angle 3.73366 / 2.70 ( 3762) metal coordination : bond 0.00241 / 0.12 ( 4) metal coordination : angle 2.93859 / 2.13 ( 6) Misc. bond : bond 0.00021 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.10 seconds wall clock time: 69 minutes 41.33 seconds (4181.33 seconds total)