Starting phenix.real_space_refine on Sun Jun 29 14:35:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.map" model { file = "/net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5y_32324/06_2025/7w5y_32324.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 166 5.49 5 S 136 5.16 5 C 21155 2.51 5 N 6150 2.21 5 O 6970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34577 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2334 Classifications: {'peptide': 300} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2380 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 10541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10541 Classifications: {'peptide': 1338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10381 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3986 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1709 Classifications: {'DNA': 83} Link IDs: {'rna3p': 82} Chain: "2" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1707 Classifications: {'DNA': 83} Link IDs: {'rna3p': 82} Chain: "K" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 912 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Time building chain proxies: 18.94, per 1000 atoms: 0.55 Number of scatterers: 34577 At special positions: 0 Unit cell: (176.445, 235.26, 164.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 166 15.00 O 6970 8.00 N 6150 7.00 C 21155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 4.3 seconds 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7374 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 50 sheets defined 38.3% alpha, 11.0% beta 26 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 12.06 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.733A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.170A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.695A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.043A pdb=" N ASP A 588 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 590' Processing helix chain 'A' and resid 592 through 600 removed outlier: 3.531A pdb=" N LYS A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 615 through 619 removed outlier: 3.512A pdb=" N LEU A 618 " --> pdb=" O GLU A 615 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 619 " --> pdb=" O VAL A 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 619' Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 45 through 50 removed outlier: 4.145A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.634A pdb=" N LEU B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.785A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.607A pdb=" N ALA B 603 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 4.236A pdb=" N GLN B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 3.676A pdb=" N THR B 630 " --> pdb=" O LYS B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.741A pdb=" N SER B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.722A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.045A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.594A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.685A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.902A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.556A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 4.267A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.545A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.666A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.516A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 432 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 470 removed outlier: 3.856A pdb=" N ALA C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 477 Processing helix chain 'C' and resid 495 through 504 removed outlier: 4.091A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.535A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.571A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.624A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.419A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 657 through 661' Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.615A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 687 removed outlier: 3.515A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 Processing helix chain 'C' and resid 710 through 713 removed outlier: 3.815A pdb=" N GLY C 713 " --> pdb=" O VAL C 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 710 through 713' Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.658A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.576A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.529A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 952 removed outlier: 3.518A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 966 removed outlier: 3.532A pdb=" N ALA C 956 " --> pdb=" O GLN C 952 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 976 removed outlier: 4.014A pdb=" N SER C 973 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 974 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 975 " --> pdb=" O PHE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.799A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1021 Processing helix chain 'C' and resid 1025 through 1036 removed outlier: 3.858A pdb=" N LEU C1029 " --> pdb=" O PHE C1025 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1129 removed outlier: 3.686A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1134 removed outlier: 3.545A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 removed outlier: 3.793A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 4.065A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.908A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1275 through 1282 removed outlier: 3.537A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1289 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.759A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.549A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.882A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 4.199A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.904A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.589A pdb=" N GLU D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.842A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 removed outlier: 4.072A pdb=" N LYS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.645A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.644A pdb=" N ALA D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 376 " --> pdb=" O MET D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.870A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.709A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.307A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.533A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 511 " --> pdb=" O VAL D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 538 removed outlier: 3.732A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.830A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 4.152A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.908A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 3.513A pdb=" N TYR D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.846A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 627 " --> pdb=" O GLN D 623 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 629 " --> pdb=" O MET D 625 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.572A pdb=" N ILE D 654 " --> pdb=" O LYS D 650 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 697 removed outlier: 5.078A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 687 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS D 695 " --> pdb=" O ASP D 691 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.506A pdb=" N ALA D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.692A pdb=" N ARG D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 787 removed outlier: 3.639A pdb=" N PHE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 804 removed outlier: 3.829A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 Processing helix chain 'D' and resid 867 through 875 Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 915 through 920 Processing helix chain 'D' and resid 920 through 928 removed outlier: 3.712A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 925 " --> pdb=" O GLN D 921 " (cutoff:3.500A) Proline residue: D 926 - end of helix No H-bonds generated for 'chain 'D' and resid 920 through 928' Processing helix chain 'D' and resid 1063 through 1067 removed outlier: 3.719A pdb=" N GLU D1066 " --> pdb=" O ASP D1063 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG D1067 " --> pdb=" O SER D1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1063 through 1067' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 3.765A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.549A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1237 removed outlier: 4.042A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1237 through 1242 removed outlier: 3.868A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.865A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1287 removed outlier: 3.974A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.681A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1335 removed outlier: 4.208A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.656A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.423A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 27 removed outlier: 3.536A pdb=" N ALA E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 4.110A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.566A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 removed outlier: 3.565A pdb=" N GLU E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 75 through 80 removed outlier: 3.552A pdb=" N GLU E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 80' Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 97 through 106 removed outlier: 3.637A pdb=" N ARG F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 134 removed outlier: 3.853A pdb=" N ILE F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 4.081A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 160 through 165 removed outlier: 4.060A pdb=" N GLY F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing helix chain 'F' and resid 222 through 237 removed outlier: 3.543A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 253 removed outlier: 4.110A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.955A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 258' Processing helix chain 'F' and resid 262 through 289 removed outlier: 3.540A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 4.245A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.717A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 removed outlier: 3.706A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 361 through 382 removed outlier: 3.914A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.837A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 390 " --> pdb=" O LEU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.891A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 446 removed outlier: 3.819A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.604A pdb=" N LYS F 462 " --> pdb=" O GLU F 458 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 463 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 485 Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.625A pdb=" N ARG F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 497 " --> pdb=" O LYS F 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 534 through 548 removed outlier: 3.971A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 563 removed outlier: 3.739A pdb=" N LYS F 557 " --> pdb=" O ALA F 553 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 578 removed outlier: 3.645A pdb=" N GLY F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 599 removed outlier: 4.151A pdb=" N GLU F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 removed outlier: 4.152A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE K 7 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN K 8 " --> pdb=" O GLN K 4 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP K 15 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 31 removed outlier: 3.868A pdb=" N VAL K 27 " --> pdb=" O ASN K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 46 removed outlier: 3.933A pdb=" N ARG K 40 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET K 41 " --> pdb=" O TYR K 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR K 44 " --> pdb=" O ARG K 40 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL K 45 " --> pdb=" O MET K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.730A pdb=" N ARG K 57 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU K 59 " --> pdb=" O ARG K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 69 removed outlier: 3.502A pdb=" N LEU K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 75 through 80 removed outlier: 3.635A pdb=" N ASP K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 96 removed outlier: 3.981A pdb=" N PHE K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE K 92 " --> pdb=" O PHE K 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG K 93 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 105 removed outlier: 4.190A pdb=" N ARG K 104 " --> pdb=" O PRO K 100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS K 105 " --> pdb=" O SER K 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 100 through 105' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.721A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 103 removed outlier: 3.644A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.783A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 202 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.783A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 103 removed outlier: 3.587A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.749A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.948A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.928A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.888A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.158A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.512A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'C' and resid 598 through 606 removed outlier: 6.603A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 638 Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.761A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.735A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.529A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.529A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 816 through 819 removed outlier: 8.190A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 836 through 841 removed outlier: 3.698A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 876 through 877 removed outlier: 3.901A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AD3, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.547A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.547A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.845A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1341 Processing sheet with id=AD8, first strand: chain 'D' and resid 103 through 112 removed outlier: 11.078A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE2, first strand: chain 'D' and resid 547 through 552 removed outlier: 3.751A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AE4, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.869A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 Processing sheet with id=AE7, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.572A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 981 through 982 Processing sheet with id=AE9, first strand: chain 'D' and resid 1026 through 1028 removed outlier: 6.705A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.913A pdb=" N ILE D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1047 through 1048 removed outlier: 4.462A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AF4, first strand: chain 'D' and resid 1187 through 1189 Processing sheet with id=AF5, first strand: chain 'D' and resid 1265 through 1266 852 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 19.61 Time building geometry restraints manager: 10.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10162 1.33 - 1.46: 7888 1.46 - 1.58: 16827 1.58 - 1.71: 330 1.71 - 1.83: 239 Bond restraints: 35446 Sorted by residual: bond pdb=" C VAL C1103 " pdb=" N PRO C1104 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.12e+00 bond pdb=" C PHE B 578 " pdb=" N ASP B 579 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.35e-02 5.49e+03 6.06e+00 bond pdb=" CA ASN C1108 " pdb=" CB ASN C1108 " ideal model delta sigma weight residual 1.525 1.553 -0.028 1.29e-02 6.01e+03 4.74e+00 bond pdb=" CA TYR C1229 " pdb=" CB TYR C1229 " ideal model delta sigma weight residual 1.527 1.475 0.052 2.48e-02 1.63e+03 4.44e+00 bond pdb=" CG LEU D 807 " pdb=" CD2 LEU D 807 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 ... (remaining 35441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 46795 2.19 - 4.38: 1570 4.38 - 6.57: 168 6.57 - 8.76: 41 8.76 - 10.95: 8 Bond angle restraints: 48582 Sorted by residual: angle pdb=" N ILE F 361 " pdb=" CA ILE F 361 " pdb=" C ILE F 361 " ideal model delta sigma weight residual 112.12 106.38 5.74 8.40e-01 1.42e+00 4.67e+01 angle pdb=" N ILE C 975 " pdb=" CA ILE C 975 " pdb=" C ILE C 975 " ideal model delta sigma weight residual 113.42 107.07 6.35 1.17e+00 7.31e-01 2.94e+01 angle pdb=" C LEU C 895 " pdb=" N THR C 896 " pdb=" CA THR C 896 " ideal model delta sigma weight residual 120.49 127.99 -7.50 1.42e+00 4.96e-01 2.79e+01 angle pdb=" C PRO D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" N VAL D 65 " pdb=" CA VAL D 65 " pdb=" C VAL D 65 " ideal model delta sigma weight residual 111.90 108.02 3.88 8.10e-01 1.52e+00 2.29e+01 ... (remaining 48577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 20310 35.50 - 70.99: 1035 70.99 - 106.49: 47 106.49 - 141.98: 2 141.98 - 177.48: 2 Dihedral angle restraints: 21396 sinusoidal: 9976 harmonic: 11420 Sorted by residual: dihedral pdb=" CA ILE D1046 " pdb=" C ILE D1046 " pdb=" N THR D1047 " pdb=" CA THR D1047 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN C1336 " pdb=" C ASN C1336 " pdb=" N ILE C1337 " pdb=" CA ILE C1337 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PRO D 584 " pdb=" C PRO D 584 " pdb=" N LYS D 585 " pdb=" CA LYS D 585 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 21393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4169 0.059 - 0.118: 1131 0.118 - 0.177: 212 0.177 - 0.236: 20 0.236 - 0.296: 5 Chirality restraints: 5537 Sorted by residual: chirality pdb=" CB ILE D 975 " pdb=" CA ILE D 975 " pdb=" CG1 ILE D 975 " pdb=" CG2 ILE D 975 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB ILE C 229 " pdb=" CA ILE C 229 " pdb=" CG1 ILE C 229 " pdb=" CG2 ILE C 229 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" P DA 2 36 " pdb=" OP1 DA 2 36 " pdb=" OP2 DA 2 36 " pdb=" O5' DA 2 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5534 not shown) Planarity restraints: 5755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 520 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO D 616 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 925 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO D 926 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 926 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 926 " -0.042 5.00e-02 4.00e+02 ... (remaining 5752 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2407 2.72 - 3.27: 31996 3.27 - 3.81: 57807 3.81 - 4.36: 69469 4.36 - 4.90: 108748 Nonbonded interactions: 270427 Sorted by model distance: nonbonded pdb=" N7 DG 2 16 " pdb=" N6 DA 2 17 " model vdw 2.180 3.200 nonbonded pdb=" O PRO A 179 " pdb=" OG1 THR A 207 " model vdw 2.211 3.040 nonbonded pdb=" N3 DG 2 19 " pdb=" N7 DG 2 20 " model vdw 2.217 3.200 nonbonded pdb=" OG1 THR D1265 " pdb=" OG SER D1303 " model vdw 2.226 3.040 nonbonded pdb=" N LEU A 629 " pdb=" OP1 DG 2 58 " model vdw 2.249 3.120 ... (remaining 270422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 233 or resid 579 through 581 or (resid 582 and ( \ name N or name CA or name C or name O or name CB )) or resid 583 through 591 or \ resid 593 through 649 or (resid 650 and (name N or name CA or name C or name O o \ r name CB )) or resid 651 through 653)) selection = (chain 'B' and (resid 6 through 233 or resid 579 through 624 or resid 630 throug \ h 653)) } 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: 0.730 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: 0.050 Extract box with map and model: 1.260 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 88.450 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 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 : 0.006 0.064 35446 Z= 0.277 Angle : 0.947 10.952 48582 Z= 0.527 Chirality : 0.055 0.296 5537 Planarity : 0.007 0.082 5755 Dihedral : 19.021 177.477 14022 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.14 % Favored : 90.81 % Rotamer: Outliers : 0.68 % Allowed : 11.48 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.10), residues: 3927 helix: -4.37 (0.07), residues: 1251 sheet: -2.68 (0.23), residues: 385 loop : -2.80 (0.11), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D1020 HIS 0.013 0.002 HIS C1116 PHE 0.028 0.003 PHE C 38 TYR 0.032 0.003 TYR C1231 ARG 0.015 0.001 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.31155 ( 896) hydrogen bonds : angle 10.93787 ( 2448) covalent geometry : bond 0.00598 (35446) covalent geometry : angle 0.94726 (48582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7427 (mttt) cc_final: 0.7000 (mmtp) REVERT: B 162 GLU cc_start: 0.4621 (mm-30) cc_final: 0.3879 (mp0) REVERT: C 275 ARG cc_start: 0.7128 (tmt170) cc_final: 0.6908 (ttp80) REVERT: C 685 MET cc_start: 0.6382 (mtm) cc_final: 0.6033 (ptt) REVERT: C 972 PHE cc_start: 0.4790 (OUTLIER) cc_final: 0.3819 (m-10) REVERT: C 1131 MET cc_start: 0.7644 (mtp) cc_final: 0.7424 (mtp) REVERT: C 1180 MET cc_start: 0.7055 (ttm) cc_final: 0.6798 (ttt) REVERT: C 1290 MET cc_start: 0.7645 (mtt) cc_final: 0.7161 (mmm) REVERT: D 330 MET cc_start: 0.7642 (mtt) cc_final: 0.7429 (mtm) REVERT: D 484 MET cc_start: 0.7424 (mtp) cc_final: 0.7053 (mtm) REVERT: D 724 MET cc_start: 0.5332 (mtm) cc_final: 0.5084 (mtt) REVERT: D 932 MET cc_start: 0.4525 (mtm) cc_final: 0.4246 (ttt) REVERT: D 1189 MET cc_start: 0.4631 (ttt) cc_final: 0.4375 (ttp) REVERT: F 273 MET cc_start: 0.7358 (tpp) cc_final: 0.7007 (mmm) REVERT: F 322 MET cc_start: 0.4957 (mtt) cc_final: 0.4516 (mmm) REVERT: F 507 MET cc_start: 0.7074 (ttm) cc_final: 0.6328 (mtm) REVERT: F 567 MET cc_start: 0.4032 (ppp) cc_final: 0.3355 (ptp) outliers start: 23 outliers final: 15 residues processed: 190 average time/residue: 0.5243 time to fit residues: 162.5707 Evaluate side-chains 142 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 0.0470 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 649 ASN C 83 GLN C 330 HIS C 526 HIS C 808 ASN D 80 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 435 GLN D 488 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 667 GLN D 680 ASN D 792 ASN D 817 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN D1218 HIS D1227 HIS D1235 ASN D1238 GLN D1279 GLN E 15 ASN E 61 ASN F 242 HIS F 309 ASN F 383 ASN F 461 ASN F 472 GLN K 56 GLN K 95 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.067341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051309 restraints weight = 412860.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052168 restraints weight = 243773.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052692 restraints weight = 174035.742| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35446 Z= 0.173 Angle : 0.684 10.714 48582 Z= 0.372 Chirality : 0.045 0.184 5537 Planarity : 0.006 0.064 5755 Dihedral : 18.504 171.304 6182 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.11), residues: 3927 helix: -3.25 (0.10), residues: 1368 sheet: -2.53 (0.22), residues: 421 loop : -2.55 (0.12), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1020 HIS 0.006 0.001 HIS F 338 PHE 0.020 0.002 PHE C 972 TYR 0.022 0.002 TYR C1231 ARG 0.006 0.001 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.06846 ( 896) hydrogen bonds : angle 6.90603 ( 2448) covalent geometry : bond 0.00374 (35446) covalent geometry : angle 0.68368 (48582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 403 MET cc_start: 0.6627 (tmm) cc_final: 0.6389 (tmm) REVERT: C 429 MET cc_start: 0.7867 (mtp) cc_final: 0.7574 (mtt) REVERT: C 459 MET cc_start: 0.6551 (mpp) cc_final: 0.6296 (mpp) REVERT: C 488 MET cc_start: 0.7252 (mmm) cc_final: 0.6895 (tpp) REVERT: C 685 MET cc_start: 0.6515 (mtm) cc_final: 0.6112 (ptp) REVERT: C 972 PHE cc_start: 0.4026 (m-10) cc_final: 0.3597 (m-10) REVERT: C 1180 MET cc_start: 0.7048 (ttm) cc_final: 0.6800 (ttt) REVERT: D 52 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6131 (mm-30) REVERT: D 237 MET cc_start: 0.7940 (mmm) cc_final: 0.7498 (mmp) REVERT: D 330 MET cc_start: 0.7768 (mtt) cc_final: 0.7552 (mtm) REVERT: D 484 MET cc_start: 0.7391 (mtp) cc_final: 0.7157 (mtm) REVERT: D 724 MET cc_start: 0.5202 (mtm) cc_final: 0.4840 (mtt) REVERT: D 817 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6273 (p-80) REVERT: D 953 LYS cc_start: 0.4417 (mmtt) cc_final: 0.3621 (ttpp) REVERT: D 1007 ASP cc_start: 0.4477 (t70) cc_final: 0.4260 (t0) REVERT: D 1095 MET cc_start: 0.2815 (ptm) cc_final: 0.2468 (tmm) REVERT: D 1334 GLU cc_start: 0.8221 (tt0) cc_final: 0.7579 (pt0) REVERT: F 161 LEU cc_start: 0.4501 (mp) cc_final: 0.4165 (tp) REVERT: F 273 MET cc_start: 0.7240 (tpp) cc_final: 0.6978 (mmm) REVERT: F 379 MET cc_start: 0.7412 (mmm) cc_final: 0.7098 (mmm) REVERT: F 507 MET cc_start: 0.7147 (ttm) cc_final: 0.6681 (mtm) REVERT: F 567 MET cc_start: 0.4138 (ppp) cc_final: 0.3365 (ptp) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.4780 time to fit residues: 119.5794 Evaluate side-chains 128 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 148 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 85 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 240 optimal weight: 0.0980 chunk 58 optimal weight: 0.0570 chunk 176 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 81 optimal weight: 20.0000 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 605 HIS C1070 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.067571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051652 restraints weight = 402031.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.052494 restraints weight = 238554.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.053053 restraints weight = 169936.265| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35446 Z= 0.109 Angle : 0.548 11.796 48582 Z= 0.298 Chirality : 0.041 0.173 5537 Planarity : 0.005 0.060 5755 Dihedral : 18.049 170.380 6182 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.12), residues: 3927 helix: -2.45 (0.11), residues: 1424 sheet: -1.88 (0.25), residues: 387 loop : -2.17 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 13 HIS 0.007 0.001 HIS F 338 PHE 0.018 0.001 PHE D 227 TYR 0.028 0.001 TYR C 291 ARG 0.009 0.000 ARG D 352 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 896) hydrogen bonds : angle 5.71961 ( 2448) covalent geometry : bond 0.00237 (35446) covalent geometry : angle 0.54840 (48582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 244 GLU cc_start: 0.6431 (tt0) cc_final: 0.6016 (mt-10) REVERT: C 403 MET cc_start: 0.6670 (tmm) cc_final: 0.6401 (tmm) REVERT: C 429 MET cc_start: 0.7955 (mtp) cc_final: 0.7629 (mtt) REVERT: C 488 MET cc_start: 0.7121 (mmm) cc_final: 0.6905 (tpp) REVERT: C 685 MET cc_start: 0.6610 (mtm) cc_final: 0.6195 (ptp) REVERT: C 972 PHE cc_start: 0.3869 (m-10) cc_final: 0.3362 (m-10) REVERT: C 1018 TYR cc_start: 0.4975 (t80) cc_final: 0.4730 (m-80) REVERT: C 1232 MET cc_start: 0.6320 (mmm) cc_final: 0.6010 (mmm) REVERT: C 1290 MET cc_start: 0.7197 (mmm) cc_final: 0.6667 (mmm) REVERT: D 29 MET cc_start: 0.7752 (tpp) cc_final: 0.7464 (mmm) REVERT: D 130 MET cc_start: 0.6734 (tpt) cc_final: 0.6261 (mmm) REVERT: D 513 MET cc_start: 0.7332 (ttm) cc_final: 0.6997 (ttm) REVERT: D 724 MET cc_start: 0.5279 (mtm) cc_final: 0.5056 (mtt) REVERT: D 822 MET cc_start: 0.5975 (mmp) cc_final: 0.5739 (mmm) REVERT: D 953 LYS cc_start: 0.4354 (mmtt) cc_final: 0.3552 (tttm) REVERT: D 979 ASN cc_start: 0.4897 (p0) cc_final: 0.3988 (t0) REVERT: D 1007 ASP cc_start: 0.4439 (t70) cc_final: 0.3708 (m-30) REVERT: D 1334 GLU cc_start: 0.7985 (tt0) cc_final: 0.7481 (pt0) REVERT: F 273 MET cc_start: 0.6963 (tpp) cc_final: 0.6699 (mmm) REVERT: F 561 MET cc_start: 0.7705 (mtt) cc_final: 0.7405 (mtt) REVERT: F 567 MET cc_start: 0.4009 (ppp) cc_final: 0.3335 (ptp) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.5211 time to fit residues: 147.0793 Evaluate side-chains 131 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 288 optimal weight: 40.0000 chunk 374 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 276 optimal weight: 0.2980 chunk 62 optimal weight: 0.0040 chunk 302 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 overall best weight: 4.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.067382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051263 restraints weight = 414551.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052082 restraints weight = 244496.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052679 restraints weight = 174078.423| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35446 Z= 0.140 Angle : 0.591 10.051 48582 Z= 0.318 Chirality : 0.042 0.185 5537 Planarity : 0.005 0.060 5755 Dihedral : 18.123 171.516 6182 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.12), residues: 3927 helix: -2.02 (0.12), residues: 1407 sheet: -1.82 (0.26), residues: 371 loop : -2.06 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1020 HIS 0.006 0.001 HIS D 430 PHE 0.018 0.002 PHE C 972 TYR 0.014 0.002 TYR C1231 ARG 0.006 0.000 ARG C1069 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 896) hydrogen bonds : angle 5.60975 ( 2448) covalent geometry : bond 0.00308 (35446) covalent geometry : angle 0.59121 (48582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 244 GLU cc_start: 0.6412 (tt0) cc_final: 0.5999 (mt-10) REVERT: C 369 MET cc_start: 0.7488 (tmm) cc_final: 0.7275 (tmm) REVERT: C 403 MET cc_start: 0.6557 (tmm) cc_final: 0.6275 (tmm) REVERT: C 429 MET cc_start: 0.7922 (mtp) cc_final: 0.7712 (mtt) REVERT: C 681 MET cc_start: 0.6346 (mtm) cc_final: 0.5960 (mtm) REVERT: C 685 MET cc_start: 0.6508 (mtm) cc_final: 0.5969 (ptp) REVERT: C 972 PHE cc_start: 0.3722 (m-10) cc_final: 0.3204 (m-10) REVERT: C 1230 MET cc_start: 0.6731 (ttm) cc_final: 0.6521 (ttp) REVERT: C 1232 MET cc_start: 0.6284 (mmm) cc_final: 0.5938 (mmm) REVERT: C 1290 MET cc_start: 0.7173 (mmm) cc_final: 0.6688 (mmm) REVERT: C 1315 MET cc_start: 0.5223 (ttt) cc_final: 0.4906 (ppp) REVERT: D 29 MET cc_start: 0.7517 (tpp) cc_final: 0.7185 (mmm) REVERT: D 130 MET cc_start: 0.6608 (tpt) cc_final: 0.5970 (mmm) REVERT: D 724 MET cc_start: 0.5180 (mtm) cc_final: 0.4924 (mtt) REVERT: D 821 MET cc_start: 0.6780 (mmm) cc_final: 0.6539 (mmm) REVERT: D 953 LYS cc_start: 0.4516 (mmtt) cc_final: 0.3588 (tttm) REVERT: D 1007 ASP cc_start: 0.4940 (t70) cc_final: 0.4620 (t0) REVERT: D 1334 GLU cc_start: 0.7978 (tt0) cc_final: 0.7548 (pt0) REVERT: F 105 MET cc_start: 0.7891 (tmm) cc_final: 0.7674 (tmm) REVERT: F 273 MET cc_start: 0.7335 (tpp) cc_final: 0.6907 (mmm) REVERT: F 507 MET cc_start: 0.6923 (ptm) cc_final: 0.6695 (ptm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4307 time to fit residues: 114.9445 Evaluate side-chains 127 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 365 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 333 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 290 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN C 604 HIS C 628 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN F 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051345 restraints weight = 415324.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.052184 restraints weight = 244526.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.052775 restraints weight = 174566.626| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35446 Z= 0.131 Angle : 0.574 12.045 48582 Z= 0.308 Chirality : 0.042 0.261 5537 Planarity : 0.004 0.058 5755 Dihedral : 18.102 172.156 6182 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.13), residues: 3927 helix: -1.65 (0.13), residues: 1411 sheet: -1.63 (0.26), residues: 370 loop : -1.95 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 13 HIS 0.005 0.001 HIS F 338 PHE 0.013 0.001 PHE C 972 TYR 0.011 0.001 TYR C1231 ARG 0.006 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 896) hydrogen bonds : angle 5.42013 ( 2448) covalent geometry : bond 0.00289 (35446) covalent geometry : angle 0.57365 (48582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 6.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.6871 (t0) cc_final: 0.6620 (t0) REVERT: C 244 GLU cc_start: 0.6255 (tt0) cc_final: 0.5706 (mt-10) REVERT: C 285 ILE cc_start: 0.5894 (tp) cc_final: 0.5609 (tt) REVERT: C 369 MET cc_start: 0.7543 (tmm) cc_final: 0.7321 (tmm) REVERT: C 403 MET cc_start: 0.6680 (tmm) cc_final: 0.6423 (tmm) REVERT: C 429 MET cc_start: 0.7891 (mtp) cc_final: 0.7663 (mtt) REVERT: C 681 MET cc_start: 0.5997 (mtm) cc_final: 0.5372 (mtm) REVERT: C 685 MET cc_start: 0.6520 (mtm) cc_final: 0.6125 (ptp) REVERT: C 972 PHE cc_start: 0.3726 (m-10) cc_final: 0.3003 (m-10) REVERT: C 1232 MET cc_start: 0.6060 (mmm) cc_final: 0.5808 (mmm) REVERT: C 1243 MET cc_start: 0.7689 (tmm) cc_final: 0.7450 (ttp) REVERT: C 1290 MET cc_start: 0.7572 (mmm) cc_final: 0.6812 (mmm) REVERT: D 29 MET cc_start: 0.7566 (tpp) cc_final: 0.7242 (mmm) REVERT: D 130 MET cc_start: 0.6395 (tpt) cc_final: 0.6077 (mmm) REVERT: D 237 MET cc_start: 0.7752 (mmm) cc_final: 0.7551 (mmm) REVERT: D 953 LYS cc_start: 0.4432 (mmtt) cc_final: 0.3530 (tttm) REVERT: D 1007 ASP cc_start: 0.4949 (t70) cc_final: 0.4711 (t0) REVERT: D 1260 MET cc_start: 0.7157 (mtm) cc_final: 0.6894 (mtm) REVERT: F 105 MET cc_start: 0.7893 (tmm) cc_final: 0.7622 (tmm) REVERT: F 273 MET cc_start: 0.7353 (tpp) cc_final: 0.6931 (mmm) REVERT: F 567 MET cc_start: 0.4349 (ppp) cc_final: 0.4130 (ppp) REVERT: K 78 MET cc_start: 0.0288 (mmt) cc_final: -0.0103 (ppp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.5677 time to fit residues: 147.2562 Evaluate side-chains 128 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 45 optimal weight: 20.0000 chunk 364 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 216 optimal weight: 0.0170 chunk 33 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 378 optimal weight: 4.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 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 = 0.3775 r_free = 0.3775 target = 0.067440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051350 restraints weight = 415494.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052204 restraints weight = 245833.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052639 restraints weight = 174889.018| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35446 Z= 0.132 Angle : 0.576 11.344 48582 Z= 0.308 Chirality : 0.042 0.205 5537 Planarity : 0.004 0.056 5755 Dihedral : 18.103 171.276 6182 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.13), residues: 3927 helix: -1.44 (0.13), residues: 1411 sheet: -1.72 (0.25), residues: 383 loop : -1.87 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 13 HIS 0.007 0.001 HIS D 545 PHE 0.017 0.001 PHE C 972 TYR 0.012 0.001 TYR D 537 ARG 0.005 0.000 ARG D 780 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 896) hydrogen bonds : angle 5.36312 ( 2448) covalent geometry : bond 0.00291 (35446) covalent geometry : angle 0.57580 (48582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 3.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7248 (t0) cc_final: 0.6844 (t0) REVERT: B 142 MET cc_start: 0.6916 (tpt) cc_final: 0.6310 (tpt) REVERT: C 244 GLU cc_start: 0.6030 (tt0) cc_final: 0.5776 (mt-10) REVERT: C 369 MET cc_start: 0.7609 (tmm) cc_final: 0.7389 (tmm) REVERT: C 403 MET cc_start: 0.6695 (tmm) cc_final: 0.6437 (tmm) REVERT: C 429 MET cc_start: 0.7909 (mtp) cc_final: 0.7679 (mtt) REVERT: C 681 MET cc_start: 0.6007 (mtm) cc_final: 0.5575 (mtm) REVERT: C 685 MET cc_start: 0.6543 (mtm) cc_final: 0.5923 (ptt) REVERT: C 972 PHE cc_start: 0.4203 (m-10) cc_final: 0.3772 (m-10) REVERT: C 1230 MET cc_start: 0.6745 (ttm) cc_final: 0.6454 (ttp) REVERT: C 1232 MET cc_start: 0.6076 (mmm) cc_final: 0.5779 (mmm) REVERT: C 1243 MET cc_start: 0.7698 (tmm) cc_final: 0.7449 (ttp) REVERT: C 1290 MET cc_start: 0.7657 (mmm) cc_final: 0.7047 (mmm) REVERT: D 29 MET cc_start: 0.7575 (tpp) cc_final: 0.7244 (mmm) REVERT: D 130 MET cc_start: 0.6328 (tpt) cc_final: 0.5972 (mmm) REVERT: D 953 LYS cc_start: 0.4437 (mmtt) cc_final: 0.3618 (tmtt) REVERT: D 1260 MET cc_start: 0.7191 (mtm) cc_final: 0.6932 (mtm) REVERT: F 105 MET cc_start: 0.7840 (tmm) cc_final: 0.7580 (tmm) REVERT: F 273 MET cc_start: 0.7319 (tpp) cc_final: 0.6876 (mmm) REVERT: K 78 MET cc_start: 0.0342 (mmt) cc_final: -0.0049 (ppp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4745 time to fit residues: 116.5994 Evaluate side-chains 124 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 231 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 chunk 261 optimal weight: 30.0000 chunk 259 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 203 optimal weight: 0.0670 chunk 391 optimal weight: 10.0000 overall best weight: 4.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.067391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051316 restraints weight = 414934.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052174 restraints weight = 246098.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052600 restraints weight = 175217.857| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35446 Z= 0.143 Angle : 0.596 11.533 48582 Z= 0.318 Chirality : 0.043 0.200 5537 Planarity : 0.005 0.056 5755 Dihedral : 18.150 171.451 6182 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3927 helix: -1.34 (0.13), residues: 1405 sheet: -1.57 (0.27), residues: 362 loop : -1.88 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1020 HIS 0.006 0.001 HIS A 160 PHE 0.017 0.002 PHE C 35 TYR 0.012 0.001 TYR D 537 ARG 0.005 0.000 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 896) hydrogen bonds : angle 5.37872 ( 2448) covalent geometry : bond 0.00316 (35446) covalent geometry : angle 0.59598 (48582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7284 (t0) cc_final: 0.6942 (t0) REVERT: B 142 MET cc_start: 0.6945 (tpt) cc_final: 0.6334 (tpt) REVERT: C 369 MET cc_start: 0.7581 (tmm) cc_final: 0.7210 (tmm) REVERT: C 403 MET cc_start: 0.6663 (tmm) cc_final: 0.6347 (tmm) REVERT: C 429 MET cc_start: 0.7938 (mtp) cc_final: 0.7696 (mtt) REVERT: C 681 MET cc_start: 0.6003 (mtm) cc_final: 0.5620 (mtm) REVERT: C 685 MET cc_start: 0.6423 (mtm) cc_final: 0.5825 (ptt) REVERT: C 972 PHE cc_start: 0.3850 (m-10) cc_final: 0.3367 (m-10) REVERT: C 1230 MET cc_start: 0.6676 (ttm) cc_final: 0.6386 (ttp) REVERT: C 1232 MET cc_start: 0.6060 (mmm) cc_final: 0.5771 (mmm) REVERT: C 1243 MET cc_start: 0.7690 (tmm) cc_final: 0.7434 (ttp) REVERT: C 1290 MET cc_start: 0.7676 (mmm) cc_final: 0.7158 (mmm) REVERT: D 29 MET cc_start: 0.7518 (tpp) cc_final: 0.7219 (mmm) REVERT: D 130 MET cc_start: 0.6316 (tpt) cc_final: 0.5953 (mmm) REVERT: D 604 MET cc_start: 0.6689 (tpp) cc_final: 0.6424 (tpp) REVERT: D 953 LYS cc_start: 0.4483 (mmtt) cc_final: 0.3675 (tmtt) REVERT: D 1260 MET cc_start: 0.7165 (mtm) cc_final: 0.6912 (mtm) REVERT: F 105 MET cc_start: 0.7833 (tmm) cc_final: 0.7541 (tmm) REVERT: F 273 MET cc_start: 0.7323 (tpp) cc_final: 0.6874 (mmm) REVERT: K 78 MET cc_start: 0.0238 (mmt) cc_final: -0.0095 (ppp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.6998 time to fit residues: 167.4702 Evaluate side-chains 124 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 388 optimal weight: 20.0000 chunk 283 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 120 GLN C1256 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN F 406 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.067301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051295 restraints weight = 419755.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052035 restraints weight = 252381.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052637 restraints weight = 184523.180| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35446 Z= 0.192 Angle : 0.684 11.974 48582 Z= 0.360 Chirality : 0.045 0.199 5537 Planarity : 0.006 0.058 5755 Dihedral : 18.395 171.769 6182 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.13), residues: 3927 helix: -1.47 (0.13), residues: 1386 sheet: -1.70 (0.27), residues: 359 loop : -2.00 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1020 HIS 0.007 0.001 HIS D 545 PHE 0.021 0.002 PHE C 35 TYR 0.017 0.002 TYR D 537 ARG 0.007 0.001 ARG F 451 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 896) hydrogen bonds : angle 5.69417 ( 2448) covalent geometry : bond 0.00426 (35446) covalent geometry : angle 0.68370 (48582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7281 (t0) cc_final: 0.6940 (t0) REVERT: B 142 MET cc_start: 0.6934 (tpt) cc_final: 0.6415 (tpt) REVERT: C 403 MET cc_start: 0.6618 (tmm) cc_final: 0.6357 (tmm) REVERT: C 429 MET cc_start: 0.8009 (mtp) cc_final: 0.7758 (mtt) REVERT: C 681 MET cc_start: 0.6059 (mtm) cc_final: 0.5687 (mtm) REVERT: C 685 MET cc_start: 0.6621 (mtm) cc_final: 0.6185 (ptt) REVERT: C 972 PHE cc_start: 0.4188 (m-10) cc_final: 0.3529 (m-10) REVERT: C 1230 MET cc_start: 0.6844 (ttm) cc_final: 0.6532 (ttp) REVERT: C 1232 MET cc_start: 0.5953 (mmm) cc_final: 0.5619 (mmm) REVERT: C 1243 MET cc_start: 0.7706 (tmm) cc_final: 0.7411 (ttp) REVERT: C 1290 MET cc_start: 0.7811 (mmm) cc_final: 0.7309 (mmm) REVERT: D 29 MET cc_start: 0.7612 (tpp) cc_final: 0.7307 (mmm) REVERT: D 180 MET cc_start: 0.7254 (ptm) cc_final: 0.6604 (ptp) REVERT: D 953 LYS cc_start: 0.4482 (mmtt) cc_final: 0.3663 (tmtt) REVERT: D 1260 MET cc_start: 0.7277 (mtm) cc_final: 0.7059 (mtm) REVERT: F 105 MET cc_start: 0.7815 (tmm) cc_final: 0.7562 (tmm) REVERT: F 273 MET cc_start: 0.7371 (tpp) cc_final: 0.6967 (mmm) REVERT: F 507 MET cc_start: 0.7814 (ptm) cc_final: 0.7532 (ptm) REVERT: K 78 MET cc_start: 0.0217 (mmt) cc_final: -0.0110 (ppp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4373 time to fit residues: 105.1556 Evaluate side-chains 123 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 22 optimal weight: 6.9990 chunk 319 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 195 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 120 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051447 restraints weight = 414366.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052315 restraints weight = 249250.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.052849 restraints weight = 176455.440| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35446 Z= 0.128 Angle : 0.588 11.437 48582 Z= 0.314 Chirality : 0.043 0.308 5537 Planarity : 0.004 0.058 5755 Dihedral : 18.185 170.146 6182 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.13), residues: 3927 helix: -1.25 (0.13), residues: 1399 sheet: -1.68 (0.26), residues: 381 loop : -1.85 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1020 HIS 0.005 0.001 HIS A 160 PHE 0.023 0.001 PHE C 972 TYR 0.017 0.001 TYR C1149 ARG 0.006 0.000 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 896) hydrogen bonds : angle 5.39296 ( 2448) covalent geometry : bond 0.00284 (35446) covalent geometry : angle 0.58835 (48582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7344 (t0) cc_final: 0.6998 (t0) REVERT: B 142 MET cc_start: 0.7128 (tpt) cc_final: 0.6533 (tpt) REVERT: C 369 MET cc_start: 0.7144 (tmm) cc_final: 0.6828 (tmm) REVERT: C 403 MET cc_start: 0.6720 (tmm) cc_final: 0.6481 (tmm) REVERT: C 429 MET cc_start: 0.8012 (mtp) cc_final: 0.7744 (mtt) REVERT: C 631 GLU cc_start: 0.4834 (tp30) cc_final: 0.4634 (tp30) REVERT: C 681 MET cc_start: 0.6023 (mtm) cc_final: 0.5626 (mtm) REVERT: C 685 MET cc_start: 0.6452 (mtm) cc_final: 0.5860 (ptt) REVERT: C 1232 MET cc_start: 0.6052 (mmm) cc_final: 0.5710 (mmm) REVERT: C 1243 MET cc_start: 0.7717 (tmm) cc_final: 0.7456 (ttp) REVERT: C 1290 MET cc_start: 0.7648 (mmm) cc_final: 0.7167 (mmm) REVERT: D 29 MET cc_start: 0.7633 (tpp) cc_final: 0.7371 (mmm) REVERT: D 484 MET cc_start: 0.7432 (mtm) cc_final: 0.7110 (mtm) REVERT: D 513 MET cc_start: 0.7506 (ttm) cc_final: 0.7298 (ttm) REVERT: D 953 LYS cc_start: 0.4490 (mmtt) cc_final: 0.3675 (tmtt) REVERT: D 1260 MET cc_start: 0.7261 (mtm) cc_final: 0.7022 (mtm) REVERT: F 105 MET cc_start: 0.7829 (tmm) cc_final: 0.7576 (tmm) REVERT: F 273 MET cc_start: 0.7304 (tpp) cc_final: 0.6918 (mmm) REVERT: F 507 MET cc_start: 0.7785 (ptm) cc_final: 0.7497 (ptm) REVERT: K 78 MET cc_start: 0.0227 (mmt) cc_final: -0.0113 (ppp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.4314 time to fit residues: 105.0298 Evaluate side-chains 124 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 228 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 230 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 382 optimal weight: 50.0000 chunk 293 optimal weight: 7.9990 chunk 216 optimal weight: 0.0670 chunk 395 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** 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 = 0.3769 r_free = 0.3769 target = 0.067347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051312 restraints weight = 414035.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052154 restraints weight = 246513.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052558 restraints weight = 176576.628| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35446 Z= 0.156 Angle : 0.630 11.300 48582 Z= 0.334 Chirality : 0.044 0.192 5537 Planarity : 0.005 0.057 5755 Dihedral : 18.294 170.988 6182 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 3927 helix: -1.26 (0.13), residues: 1396 sheet: -1.61 (0.27), residues: 367 loop : -1.90 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1020 HIS 0.007 0.001 HIS A 160 PHE 0.023 0.002 PHE C 972 TYR 0.021 0.002 TYR C1149 ARG 0.007 0.001 ARG D1203 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 896) hydrogen bonds : angle 5.50526 ( 2448) covalent geometry : bond 0.00347 (35446) covalent geometry : angle 0.63037 (48582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7320 (t0) cc_final: 0.6963 (t0) REVERT: B 142 MET cc_start: 0.6886 (tpt) cc_final: 0.6313 (tpt) REVERT: C 369 MET cc_start: 0.7143 (tmm) cc_final: 0.6936 (tmm) REVERT: C 403 MET cc_start: 0.6561 (tmm) cc_final: 0.6265 (tmm) REVERT: C 429 MET cc_start: 0.7946 (mtp) cc_final: 0.7691 (mtt) REVERT: C 515 MET cc_start: 0.5902 (tpp) cc_final: 0.5608 (tpp) REVERT: C 681 MET cc_start: 0.6020 (mtm) cc_final: 0.5657 (mtm) REVERT: C 685 MET cc_start: 0.6432 (mtm) cc_final: 0.5870 (ptt) REVERT: C 1230 MET cc_start: 0.6701 (ttm) cc_final: 0.6378 (ttp) REVERT: C 1232 MET cc_start: 0.5940 (mmm) cc_final: 0.5564 (mmm) REVERT: C 1243 MET cc_start: 0.7685 (tmm) cc_final: 0.7421 (ttp) REVERT: C 1290 MET cc_start: 0.7685 (mmm) cc_final: 0.7344 (mmm) REVERT: D 29 MET cc_start: 0.7466 (tpp) cc_final: 0.7086 (mmm) REVERT: D 180 MET cc_start: 0.7221 (ptm) cc_final: 0.6502 (ptp) REVERT: D 237 MET cc_start: 0.7957 (mmm) cc_final: 0.7358 (ttt) REVERT: D 953 LYS cc_start: 0.4489 (mmtt) cc_final: 0.3658 (tmtt) REVERT: D 1260 MET cc_start: 0.7238 (mtm) cc_final: 0.7026 (mtm) REVERT: F 105 MET cc_start: 0.7806 (tmm) cc_final: 0.7556 (tmm) REVERT: F 273 MET cc_start: 0.7330 (tpp) cc_final: 0.6898 (mmm) REVERT: F 286 LEU cc_start: 0.6647 (mp) cc_final: 0.6394 (tp) REVERT: F 507 MET cc_start: 0.7911 (ptm) cc_final: 0.7547 (ptm) REVERT: K 78 MET cc_start: 0.0223 (mmt) cc_final: -0.0113 (ppp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4387 time to fit residues: 103.9827 Evaluate side-chains 127 residues out of total 3401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 158 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 281 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 260 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.067351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051410 restraints weight = 413789.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052240 restraints weight = 249582.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052745 restraints weight = 176133.555| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35446 Z= 0.140 Angle : 0.603 11.168 48582 Z= 0.320 Chirality : 0.043 0.188 5537 Planarity : 0.005 0.057 5755 Dihedral : 18.280 171.020 6182 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3927 helix: -1.18 (0.13), residues: 1389 sheet: -1.55 (0.27), residues: 365 loop : -1.85 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1020 HIS 0.006 0.001 HIS A 160 PHE 0.021 0.001 PHE C 972 TYR 0.021 0.001 TYR C1149 ARG 0.005 0.000 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 896) hydrogen bonds : angle 5.43869 ( 2448) covalent geometry : bond 0.00312 (35446) covalent geometry : angle 0.60278 (48582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12003.14 seconds wall clock time: 217 minutes 21.95 seconds (13041.95 seconds total)