Starting phenix.real_space_refine on Fri Mar 6 08:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py3_13709/03_2026/7py3_13709.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18090 2.51 5 N 5265 2.21 5 O 5831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29362 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2076 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 6, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Chain: "D" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14877 SG CYS D 70 81.855 36.090 89.479 1.00155.50 S ATOM 14891 SG CYS D 72 82.055 32.908 91.677 1.00162.97 S ATOM 15023 SG CYS D 88 83.060 35.046 93.686 1.00154.73 S ATOM 21276 SG CYS D 888 91.951 100.742 103.503 1.00108.58 S ATOM 21327 SG CYS D 895 88.541 99.695 102.203 1.00101.00 S ATOM 21348 SG CYS D 898 91.085 103.285 101.485 1.00 99.07 S Time building chain proxies: 5.64, per 1000 atoms: 0.19 Number of scatterers: 29362 At special positions: 0 Unit cell: (186.39, 154.78, 179.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 68 15.00 Mg 1 11.99 O 5831 8.00 N 5265 7.00 C 18090 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: 5.85 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 45 sheets defined 37.0% alpha, 12.5% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.758A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.994A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 48 removed outlier: 3.860A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.415A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.142A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.538A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.511A pdb=" N ASP B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.601A pdb=" N SER B 266 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 308 removed outlier: 4.215A pdb=" N THR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.966A pdb=" N ALA B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 40 removed outlier: 3.663A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.558A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.590A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.708A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.567A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.501A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.259A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.647A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.357A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.569A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.100A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.798A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.777A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.961A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.358A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.702A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.819A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.619A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.744A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.523A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.841A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.786A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.587A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 4.058A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.862A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 4.169A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.636A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.698A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.770A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.047A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.836A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 264 through 286 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 408 through 416 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: 3.902A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.511A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.928A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.786A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.540A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.944A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.658A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.501A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.887A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 removed outlier: 3.526A pdb=" N GLN D 929 " --> pdb=" O PRO D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 926 through 929' Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.658A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.758A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 4.341A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1289 removed outlier: 3.529A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.121A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.640A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.042A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.819A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.525A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.624A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.612A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.744A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 removed outlier: 3.513A pdb=" N ALA F 79 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 113 through 131 removed outlier: 3.572A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.528A pdb=" N ARG F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 314 through 319 removed outlier: 3.704A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.763A pdb=" N LEU F 327 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 330 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 364 removed outlier: 3.961A pdb=" N ILE F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 371 Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.792A pdb=" N ALA F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 420 Processing helix chain 'F' and resid 442 through 451 removed outlier: 3.724A pdb=" N ALA F 445 " --> pdb=" O ARG F 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F 446 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA F 449 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA F 450 " --> pdb=" O LYS F 447 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 451 " --> pdb=" O LEU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 462 removed outlier: 3.514A pdb=" N ALA F 460 " --> pdb=" O GLU F 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN F 462 " --> pdb=" O LEU F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 removed outlier: 3.886A pdb=" N ASN F 487 " --> pdb=" O MET F 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 19 removed outlier: 5.453A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.707A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.577A pdb=" N VAL A 110 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.701A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.701A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 removed outlier: 4.192A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 110 removed outlier: 4.224A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.620A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.300A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.747A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 159 removed outlier: 5.726A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE C 188 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 186 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.037A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 333 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.771A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.167A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.957A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.675A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.558A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.889A pdb=" N ALA C 716 " --> pdb=" O ALA C 784 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 750 removed outlier: 7.061A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.781A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 5.823A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.696A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 467 " --> pdb=" O ASN D 424 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 469 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.696A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.598A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.804A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD3, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.638A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'D' and resid 552 through 556 removed outlier: 3.698A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'D' and resid 849 through 850 removed outlier: 4.083A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.704A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE1, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE2, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 4.075A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.567A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1189 Processing sheet with id=AE5, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 5.174A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN D1268 " --> pdb=" O THR D1301 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.619A pdb=" N THR F 58 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 138 through 141 Processing sheet with id=AE8, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.449A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 221 through 222 removed outlier: 3.714A pdb=" N LYS F 239 " --> pdb=" O GLU F 222 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9867 1.34 - 1.46: 5030 1.46 - 1.58: 14679 1.58 - 1.70: 132 1.70 - 1.82: 182 Bond restraints: 29890 Sorted by residual: bond pdb=" CA CYS B 176 " pdb=" CB CYS B 176 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.76e-02 3.23e+03 3.56e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CB ASP B 197 " pdb=" CG ASP B 197 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.11e+00 bond pdb=" C GLU B 29 " pdb=" N PRO B 30 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C ALA F 11 " pdb=" N VAL F 12 " ideal model delta sigma weight residual 1.329 1.348 -0.019 1.40e-02 5.10e+03 1.76e+00 ... (remaining 29885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 40117 2.27 - 4.54: 563 4.54 - 6.81: 82 6.81 - 9.07: 17 9.07 - 11.34: 3 Bond angle restraints: 40782 Sorted by residual: angle pdb=" N VAL E 6 " pdb=" CA VAL E 6 " pdb=" C VAL E 6 " ideal model delta sigma weight residual 113.20 106.35 6.85 9.60e-01 1.09e+00 5.10e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 130.10 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" N GLU C1012 " pdb=" CA GLU C1012 " pdb=" CB GLU C1012 " ideal model delta sigma weight residual 110.39 117.87 -7.48 1.66e+00 3.63e-01 2.03e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 129.68 -7.98 1.80e+00 3.09e-01 1.97e+01 angle pdb=" C GLU E 42 " pdb=" N ASN E 43 " pdb=" CA ASN E 43 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 ... (remaining 40777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.73: 17295 28.73 - 57.45: 765 57.45 - 86.18: 104 86.18 - 114.90: 5 114.90 - 143.63: 5 Dihedral angle restraints: 18174 sinusoidal: 7294 harmonic: 10880 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 -130.22 -49.78 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual 200.00 125.69 74.31 1 1.50e+01 4.44e-03 3.11e+01 ... (remaining 18171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3450 0.045 - 0.090: 993 0.090 - 0.135: 278 0.135 - 0.180: 28 0.180 - 0.225: 8 Chirality restraints: 4757 Sorted by residual: chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 61 " pdb=" CA ILE B 61 " pdb=" CG1 ILE B 61 " pdb=" CG2 ILE B 61 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4754 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " -0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO B 30 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO C 58 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO C 552 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.040 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 362 2.63 - 3.20: 25750 3.20 - 3.76: 44725 3.76 - 4.33: 56894 4.33 - 4.90: 92151 Nonbonded interactions: 219882 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.060 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.070 2.170 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.136 2.496 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.168 2.496 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.198 3.040 ... (remaining 219877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29896 Z= 0.138 Angle : 0.673 11.344 40782 Z= 0.357 Chirality : 0.046 0.225 4757 Planarity : 0.005 0.096 5164 Dihedral : 15.989 143.627 11156 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.04 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3767 helix: -0.18 (0.15), residues: 1162 sheet: -1.28 (0.25), residues: 407 loop : -1.98 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.029 0.001 TYR B 177 PHE 0.024 0.001 PHE C 389 TRP 0.014 0.001 TRP C1276 HIS 0.008 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00285 (29890) covalent geometry : angle 0.67310 (40782) hydrogen bonds : bond 0.20242 ( 1051) hydrogen bonds : angle 6.86976 ( 2913) metal coordination : bond 0.00259 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.7752 (mm) cc_final: 0.7507 (mm) REVERT: B 29 GLU cc_start: 0.7639 (tt0) cc_final: 0.7198 (mt-10) REVERT: B 127 GLN cc_start: 0.9302 (pm20) cc_final: 0.9013 (pm20) REVERT: C 47 TYR cc_start: 0.1638 (m-80) cc_final: -0.0655 (m-80) REVERT: C 187 GLU cc_start: 0.7845 (tp30) cc_final: 0.7336 (tt0) REVERT: C 337 PHE cc_start: 0.8611 (t80) cc_final: 0.8265 (t80) REVERT: C 488 MET cc_start: 0.8317 (mmm) cc_final: 0.7982 (mmm) REVERT: C 770 CYS cc_start: 0.8199 (t) cc_final: 0.7552 (t) REVERT: C 785 ASP cc_start: 0.7583 (m-30) cc_final: 0.6919 (m-30) REVERT: C 1023 HIS cc_start: 0.8881 (m90) cc_final: 0.8529 (m90) REVERT: C 1034 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8251 (ttp80) REVERT: C 1080 ASN cc_start: 0.8380 (m110) cc_final: 0.8077 (m-40) REVERT: D 466 MET cc_start: 0.7868 (mtt) cc_final: 0.7642 (mtt) REVERT: D 832 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8835 (mmmt) REVERT: E 46 THR cc_start: 0.9145 (p) cc_final: 0.8765 (t) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.1706 time to fit residues: 85.4437 Evaluate side-chains 223 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087949 restraints weight = 60211.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091099 restraints weight = 31201.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093179 restraints weight = 20373.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094587 restraints weight = 15573.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095433 restraints weight = 13183.562| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29896 Z= 0.151 Angle : 0.589 9.260 40782 Z= 0.308 Chirality : 0.043 0.202 4757 Planarity : 0.005 0.095 5164 Dihedral : 14.513 148.132 4879 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.92 % Allowed : 8.86 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3767 helix: 0.38 (0.15), residues: 1200 sheet: -1.34 (0.26), residues: 382 loop : -1.91 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 994 TYR 0.020 0.001 TYR B 177 PHE 0.015 0.001 PHE C 57 TRP 0.017 0.001 TRP C1276 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00345 (29890) covalent geometry : angle 0.58860 (40782) hydrogen bonds : bond 0.05033 ( 1051) hydrogen bonds : angle 4.93153 ( 2913) metal coordination : bond 0.00280 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 168 ILE cc_start: 0.7619 (mm) cc_final: 0.7360 (mm) REVERT: B 29 GLU cc_start: 0.7621 (tt0) cc_final: 0.7163 (mt-10) REVERT: B 127 GLN cc_start: 0.9263 (pm20) cc_final: 0.9059 (pm20) REVERT: B 177 TYR cc_start: 0.7214 (p90) cc_final: 0.6696 (p90) REVERT: C 47 TYR cc_start: 0.1707 (m-80) cc_final: -0.0590 (m-80) REVERT: C 187 GLU cc_start: 0.7857 (tp30) cc_final: 0.7458 (tt0) REVERT: C 337 PHE cc_start: 0.8659 (t80) cc_final: 0.8252 (t80) REVERT: C 369 MET cc_start: 0.7900 (ppp) cc_final: 0.7667 (ppp) REVERT: C 429 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8392 (mpp) REVERT: C 488 MET cc_start: 0.8367 (mmm) cc_final: 0.8139 (mmm) REVERT: C 588 GLU cc_start: 0.8416 (pt0) cc_final: 0.8069 (pt0) REVERT: C 770 CYS cc_start: 0.8367 (t) cc_final: 0.7716 (t) REVERT: C 785 ASP cc_start: 0.7584 (m-30) cc_final: 0.6917 (m-30) REVERT: C 1023 HIS cc_start: 0.9062 (m90) cc_final: 0.8702 (m90) REVERT: C 1034 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8302 (ttp80) REVERT: C 1080 ASN cc_start: 0.8386 (m110) cc_final: 0.8151 (m-40) REVERT: C 1092 THR cc_start: 0.9079 (p) cc_final: 0.8815 (p) REVERT: C 1106 ARG cc_start: 0.8707 (mpp80) cc_final: 0.7724 (mtm-85) REVERT: D 17 PHE cc_start: 0.8235 (p90) cc_final: 0.7705 (p90) REVERT: D 29 MET cc_start: 0.7799 (mtp) cc_final: 0.7588 (ttm) REVERT: D 192 MET cc_start: 0.8852 (ptm) cc_final: 0.8505 (ppp) REVERT: D 404 GLU cc_start: 0.8554 (pm20) cc_final: 0.8208 (mp0) REVERT: D 466 MET cc_start: 0.7495 (mtt) cc_final: 0.7252 (mtt) outliers start: 25 outliers final: 19 residues processed: 262 average time/residue: 0.1746 time to fit residues: 76.0522 Evaluate side-chains 236 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 54 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 374 optimal weight: 40.0000 chunk 245 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089014 restraints weight = 58114.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092207 restraints weight = 29576.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094346 restraints weight = 19019.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095694 restraints weight = 14331.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096607 restraints weight = 12084.971| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29896 Z= 0.127 Angle : 0.550 13.153 40782 Z= 0.286 Chirality : 0.042 0.201 4757 Planarity : 0.004 0.092 5164 Dihedral : 14.388 149.613 4879 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.46 % Allowed : 11.42 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3767 helix: 0.64 (0.15), residues: 1213 sheet: -1.12 (0.27), residues: 382 loop : -1.86 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 634 TYR 0.015 0.001 TYR C1018 PHE 0.013 0.001 PHE D 17 TRP 0.018 0.001 TRP C1276 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00290 (29890) covalent geometry : angle 0.55032 (40782) hydrogen bonds : bond 0.04485 ( 1051) hydrogen bonds : angle 4.49490 ( 2913) metal coordination : bond 0.00212 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 168 ILE cc_start: 0.7636 (mm) cc_final: 0.7367 (mm) REVERT: B 29 GLU cc_start: 0.7590 (tt0) cc_final: 0.7258 (mt-10) REVERT: B 177 TYR cc_start: 0.7355 (p90) cc_final: 0.6623 (p90) REVERT: C 47 TYR cc_start: 0.1654 (m-80) cc_final: -0.0623 (m-80) REVERT: C 164 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8920 (m) REVERT: C 187 GLU cc_start: 0.7872 (tp30) cc_final: 0.7536 (tt0) REVERT: C 337 PHE cc_start: 0.8654 (t80) cc_final: 0.8270 (t80) REVERT: C 488 MET cc_start: 0.8381 (mmm) cc_final: 0.8151 (mmm) REVERT: C 588 GLU cc_start: 0.8434 (pt0) cc_final: 0.8119 (pt0) REVERT: C 770 CYS cc_start: 0.8419 (t) cc_final: 0.7776 (t) REVERT: C 785 ASP cc_start: 0.7449 (m-30) cc_final: 0.6879 (m-30) REVERT: C 1080 ASN cc_start: 0.8472 (m110) cc_final: 0.8269 (m-40) REVERT: C 1092 THR cc_start: 0.9100 (p) cc_final: 0.8862 (p) REVERT: C 1106 ARG cc_start: 0.8678 (mpp80) cc_final: 0.7652 (mtm-85) REVERT: C 1273 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: D 29 MET cc_start: 0.7819 (mtp) cc_final: 0.7611 (ttm) REVERT: D 192 MET cc_start: 0.8788 (ptm) cc_final: 0.8552 (ppp) REVERT: D 466 MET cc_start: 0.7598 (mtt) cc_final: 0.7274 (mtt) outliers start: 40 outliers final: 25 residues processed: 258 average time/residue: 0.1657 time to fit residues: 71.4695 Evaluate side-chains 246 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 207 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 333 optimal weight: 50.0000 chunk 230 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082479 restraints weight = 61263.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085335 restraints weight = 32440.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087233 restraints weight = 21644.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088435 restraints weight = 16822.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089241 restraints weight = 14479.803| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 29896 Z= 0.306 Angle : 0.716 10.014 40782 Z= 0.368 Chirality : 0.047 0.230 4757 Planarity : 0.005 0.102 5164 Dihedral : 14.538 152.298 4879 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 2.56 % Allowed : 14.54 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3767 helix: 0.51 (0.15), residues: 1208 sheet: -1.35 (0.26), residues: 385 loop : -1.99 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 247 TYR 0.017 0.002 TYR A 177 PHE 0.023 0.002 PHE B 231 TRP 0.010 0.002 TRP C1276 HIS 0.008 0.002 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00729 (29890) covalent geometry : angle 0.71589 (40782) hydrogen bonds : bond 0.05393 ( 1051) hydrogen bonds : angle 4.79618 ( 2913) metal coordination : bond 0.01287 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 220 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8043 (p90) REVERT: B 29 GLU cc_start: 0.7624 (tt0) cc_final: 0.7420 (mt-10) REVERT: B 177 TYR cc_start: 0.7767 (p90) cc_final: 0.6726 (p90) REVERT: C 47 TYR cc_start: 0.2361 (m-80) cc_final: -0.0280 (m-80) REVERT: C 187 GLU cc_start: 0.8127 (tp30) cc_final: 0.7812 (tt0) REVERT: C 337 PHE cc_start: 0.8813 (t80) cc_final: 0.8198 (t80) REVERT: C 488 MET cc_start: 0.8363 (mmm) cc_final: 0.8112 (mmm) REVERT: C 572 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (mp) REVERT: C 1027 LYS cc_start: 0.9256 (ptmt) cc_final: 0.8815 (pttm) REVERT: C 1056 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8339 (m) REVERT: C 1229 TYR cc_start: 0.8895 (m-80) cc_final: 0.8351 (m-80) REVERT: C 1243 MET cc_start: 0.8733 (tmm) cc_final: 0.8385 (tmm) REVERT: C 1273 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8614 (mtm) REVERT: D 192 MET cc_start: 0.8811 (ptm) cc_final: 0.8563 (ppp) REVERT: D 466 MET cc_start: 0.7980 (mtt) cc_final: 0.7656 (mtt) REVERT: D 497 GLU cc_start: 0.8446 (pt0) cc_final: 0.7892 (pm20) REVERT: D 1370 MET cc_start: 0.8641 (tpp) cc_final: 0.8107 (tmm) outliers start: 70 outliers final: 42 residues processed: 274 average time/residue: 0.1652 time to fit residues: 76.0071 Evaluate side-chains 251 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 136 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 chunk 330 optimal weight: 10.0000 chunk 346 optimal weight: 0.0020 chunk 314 optimal weight: 3.9990 chunk 363 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 824 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1080 ASN C1268 GLN D 158 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 875 ASN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082872 restraints weight = 59710.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085644 restraints weight = 31335.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087530 restraints weight = 20804.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088734 restraints weight = 16062.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089457 restraints weight = 13711.631| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 29896 Z= 0.305 Angle : 0.706 8.905 40782 Z= 0.365 Chirality : 0.047 0.350 4757 Planarity : 0.005 0.100 5164 Dihedral : 14.618 155.112 4879 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.57 % Favored : 91.35 % Rotamer: Outliers : 3.55 % Allowed : 15.93 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3767 helix: 0.43 (0.16), residues: 1201 sheet: -1.59 (0.25), residues: 401 loop : -2.08 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 634 TYR 0.016 0.002 TYR C 726 PHE 0.024 0.002 PHE B 231 TRP 0.020 0.002 TRP C1276 HIS 0.006 0.002 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00720 (29890) covalent geometry : angle 0.70638 (40782) hydrogen bonds : bond 0.05229 ( 1051) hydrogen bonds : angle 4.79529 ( 2913) metal coordination : bond 0.01293 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8191 (p90) REVERT: B 177 TYR cc_start: 0.7982 (p90) cc_final: 0.6799 (p90) REVERT: C 47 TYR cc_start: 0.2331 (m-80) cc_final: -0.0062 (m-80) REVERT: C 121 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: C 187 GLU cc_start: 0.8179 (tp30) cc_final: 0.7810 (tt0) REVERT: C 337 PHE cc_start: 0.8857 (t80) cc_final: 0.8319 (t80) REVERT: C 488 MET cc_start: 0.8467 (mmm) cc_final: 0.8255 (mmm) REVERT: C 1056 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8386 (m) REVERT: C 1164 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: C 1229 TYR cc_start: 0.8914 (m-80) cc_final: 0.8424 (m-80) REVERT: C 1243 MET cc_start: 0.8764 (tmm) cc_final: 0.8398 (tmm) REVERT: C 1268 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7916 (mm-40) REVERT: C 1273 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: D 192 MET cc_start: 0.8843 (ptm) cc_final: 0.8596 (ppp) REVERT: D 466 MET cc_start: 0.7855 (mtt) cc_final: 0.7561 (mtt) REVERT: D 497 GLU cc_start: 0.8416 (pt0) cc_final: 0.7889 (pm20) REVERT: D 551 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7270 (ptm-80) REVERT: D 960 LEU cc_start: 0.8768 (mm) cc_final: 0.8097 (tp) REVERT: D 1370 MET cc_start: 0.8597 (tpp) cc_final: 0.8087 (tmm) REVERT: E 3 ARG cc_start: 0.6875 (tpm170) cc_final: 0.6657 (tpm170) REVERT: E 72 GLN cc_start: 0.8824 (pp30) cc_final: 0.8567 (pp30) outliers start: 97 outliers final: 56 residues processed: 294 average time/residue: 0.1681 time to fit residues: 82.8982 Evaluate side-chains 269 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 365 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 chunk 288 optimal weight: 50.0000 chunk 179 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 338 optimal weight: 50.0000 chunk 221 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1313 HIS D 45 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084948 restraints weight = 61035.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089298 restraints weight = 34201.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089552 restraints weight = 20858.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090308 restraints weight = 15390.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090514 restraints weight = 14399.161| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29896 Z= 0.180 Angle : 0.605 8.950 40782 Z= 0.314 Chirality : 0.044 0.260 4757 Planarity : 0.004 0.094 5164 Dihedral : 14.566 155.698 4879 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 2.93 % Allowed : 17.21 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3767 helix: 0.62 (0.16), residues: 1200 sheet: -1.33 (0.25), residues: 391 loop : -2.02 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 744 TYR 0.018 0.002 TYR C1018 PHE 0.015 0.001 PHE B 231 TRP 0.027 0.002 TRP C1276 HIS 0.016 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00423 (29890) covalent geometry : angle 0.60521 (40782) hydrogen bonds : bond 0.04666 ( 1051) hydrogen bonds : angle 4.49776 ( 2913) metal coordination : bond 0.00764 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8165 (p90) REVERT: B 29 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 122 GLU cc_start: 0.8094 (mp0) cc_final: 0.7469 (mp0) REVERT: B 177 TYR cc_start: 0.7835 (p90) cc_final: 0.6726 (p90) REVERT: C 47 TYR cc_start: 0.1957 (m-80) cc_final: 0.0375 (m-80) REVERT: C 187 GLU cc_start: 0.8140 (tp30) cc_final: 0.7808 (tt0) REVERT: C 337 PHE cc_start: 0.8789 (t80) cc_final: 0.8287 (t80) REVERT: C 447 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7883 (t70) REVERT: C 488 MET cc_start: 0.8457 (mmm) cc_final: 0.8220 (mmm) REVERT: C 714 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9070 (p) REVERT: C 1027 LYS cc_start: 0.9211 (ptmt) cc_final: 0.8812 (pttm) REVERT: C 1056 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8346 (m) REVERT: C 1107 MET cc_start: 0.8236 (tpt) cc_final: 0.7733 (tpt) REVERT: C 1164 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: C 1229 TYR cc_start: 0.8891 (m-80) cc_final: 0.8298 (m-80) REVERT: C 1243 MET cc_start: 0.8750 (tmm) cc_final: 0.8312 (tmm) REVERT: C 1268 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7939 (mm-40) REVERT: C 1273 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8375 (mtm) REVERT: D 192 MET cc_start: 0.8755 (ptm) cc_final: 0.8525 (ppp) REVERT: D 330 MET cc_start: 0.7650 (ttt) cc_final: 0.7424 (ttt) REVERT: D 466 MET cc_start: 0.7723 (mtt) cc_final: 0.7457 (mtt) REVERT: D 551 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.6982 (ptm-80) REVERT: D 897 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: D 1370 MET cc_start: 0.8584 (tpp) cc_final: 0.8074 (tmm) outliers start: 80 outliers final: 52 residues processed: 281 average time/residue: 0.1672 time to fit residues: 78.7055 Evaluate side-chains 266 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 349 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1023 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 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 = 0.3992 r_free = 0.3992 target = 0.135750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083760 restraints weight = 61586.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088015 restraints weight = 35028.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088303 restraints weight = 21247.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089000 restraints weight = 15819.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089312 restraints weight = 14948.502| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29896 Z= 0.241 Angle : 0.657 9.216 40782 Z= 0.338 Chirality : 0.045 0.254 4757 Planarity : 0.005 0.095 5164 Dihedral : 14.594 154.794 4879 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.92 % Favored : 91.00 % Rotamer: Outliers : 3.41 % Allowed : 17.72 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3767 helix: 0.54 (0.15), residues: 1211 sheet: -1.49 (0.25), residues: 396 loop : -2.04 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1034 TYR 0.035 0.002 TYR C1281 PHE 0.017 0.002 PHE B 231 TRP 0.023 0.002 TRP C1276 HIS 0.008 0.001 HIS C1313 Details of bonding type rmsd covalent geometry : bond 0.00570 (29890) covalent geometry : angle 0.65722 (40782) hydrogen bonds : bond 0.04906 ( 1051) hydrogen bonds : angle 4.55447 ( 2913) metal coordination : bond 0.01011 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 213 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8230 (p90) REVERT: B 29 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7368 (mt-10) REVERT: B 122 GLU cc_start: 0.8097 (mp0) cc_final: 0.7470 (mp0) REVERT: B 172 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9060 (pp) REVERT: B 177 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6793 (p90) REVERT: C 47 TYR cc_start: 0.2188 (m-80) cc_final: 0.0449 (m-80) REVERT: C 187 GLU cc_start: 0.8156 (tp30) cc_final: 0.7825 (tt0) REVERT: C 337 PHE cc_start: 0.8882 (t80) cc_final: 0.8391 (t80) REVERT: C 429 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8563 (mpp) REVERT: C 447 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7907 (t70) REVERT: C 488 MET cc_start: 0.8468 (mmm) cc_final: 0.8138 (mmm) REVERT: C 714 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9069 (p) REVERT: C 1027 LYS cc_start: 0.9210 (ptmt) cc_final: 0.8835 (pttm) REVERT: C 1056 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8350 (m) REVERT: C 1164 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: C 1229 TYR cc_start: 0.8914 (m-80) cc_final: 0.8325 (m-80) REVERT: C 1232 MET cc_start: 0.8426 (ttm) cc_final: 0.8141 (ttm) REVERT: C 1243 MET cc_start: 0.8790 (tmm) cc_final: 0.8272 (tmm) REVERT: C 1268 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7968 (mm-40) REVERT: C 1273 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: D 192 MET cc_start: 0.8808 (ptm) cc_final: 0.8585 (ppp) REVERT: D 466 MET cc_start: 0.7769 (mtt) cc_final: 0.7502 (mtt) REVERT: D 497 GLU cc_start: 0.8559 (pt0) cc_final: 0.7828 (pm20) REVERT: D 551 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7044 (ptm-80) REVERT: D 897 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7728 (t-90) REVERT: D 960 LEU cc_start: 0.8642 (mm) cc_final: 0.8119 (tp) REVERT: D 1028 ILE cc_start: 0.8951 (mm) cc_final: 0.8627 (tp) REVERT: D 1370 MET cc_start: 0.8630 (tpp) cc_final: 0.8092 (tmm) outliers start: 93 outliers final: 65 residues processed: 286 average time/residue: 0.1679 time to fit residues: 80.7290 Evaluate side-chains 280 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.7980 chunk 310 optimal weight: 0.0370 chunk 176 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 368 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 371 optimal weight: 40.0000 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.138806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085576 restraints weight = 60873.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088635 restraints weight = 31271.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090668 restraints weight = 20482.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092041 restraints weight = 15766.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.092767 restraints weight = 13430.711| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29896 Z= 0.124 Angle : 0.574 8.992 40782 Z= 0.297 Chirality : 0.043 0.227 4757 Planarity : 0.004 0.092 5164 Dihedral : 14.499 156.078 4879 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 2.56 % Allowed : 19.30 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3767 helix: 0.78 (0.16), residues: 1206 sheet: -1.18 (0.26), residues: 388 loop : -1.93 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1034 TYR 0.018 0.001 TYR C1281 PHE 0.015 0.001 PHE C 57 TRP 0.031 0.002 TRP C1276 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00286 (29890) covalent geometry : angle 0.57416 (40782) hydrogen bonds : bond 0.04239 ( 1051) hydrogen bonds : angle 4.23255 ( 2913) metal coordination : bond 0.00341 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7970 (p90) REVERT: B 29 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 177 TYR cc_start: 0.7715 (p90) cc_final: 0.6665 (p90) REVERT: C 47 TYR cc_start: 0.1780 (m-80) cc_final: 0.0060 (m-80) REVERT: C 187 GLU cc_start: 0.8059 (tp30) cc_final: 0.7757 (tt0) REVERT: C 291 TYR cc_start: 0.8438 (t80) cc_final: 0.8125 (t80) REVERT: C 337 PHE cc_start: 0.8793 (t80) cc_final: 0.8418 (t80) REVERT: C 429 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8540 (mpp) REVERT: C 447 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7835 (t-170) REVERT: C 488 MET cc_start: 0.8477 (mmm) cc_final: 0.8162 (mmm) REVERT: C 588 GLU cc_start: 0.8409 (pt0) cc_final: 0.8045 (pt0) REVERT: C 714 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9090 (p) REVERT: C 1023 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8123 (t-170) REVERT: C 1027 LYS cc_start: 0.9236 (ptmt) cc_final: 0.8935 (ptpp) REVERT: C 1034 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8395 (ttp80) REVERT: C 1107 MET cc_start: 0.8373 (tpt) cc_final: 0.7703 (tpt) REVERT: C 1164 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: C 1229 TYR cc_start: 0.8864 (m-80) cc_final: 0.8196 (m-80) REVERT: C 1232 MET cc_start: 0.8414 (ttm) cc_final: 0.8090 (ttm) REVERT: C 1243 MET cc_start: 0.8793 (tmm) cc_final: 0.8301 (tmm) REVERT: C 1268 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7784 (mm-40) REVERT: C 1273 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: D 75 TYR cc_start: 0.8212 (m-10) cc_final: 0.7977 (m-80) REVERT: D 245 LEU cc_start: 0.8648 (tp) cc_final: 0.8420 (mp) REVERT: D 330 MET cc_start: 0.7642 (ttt) cc_final: 0.7376 (ttt) REVERT: D 513 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8757 (ttp) REVERT: D 551 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.6936 (ptm-80) REVERT: D 897 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7775 (t-90) REVERT: D 960 LEU cc_start: 0.8709 (mm) cc_final: 0.8211 (tp) REVERT: D 1028 ILE cc_start: 0.9009 (mm) cc_final: 0.8697 (tp) REVERT: D 1370 MET cc_start: 0.8490 (tpp) cc_final: 0.8054 (tmm) outliers start: 70 outliers final: 53 residues processed: 276 average time/residue: 0.1696 time to fit residues: 78.3340 Evaluate side-chains 275 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 44 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 293 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 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 = 0.4025 r_free = 0.4025 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086567 restraints weight = 60858.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090924 restraints weight = 34119.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091246 restraints weight = 20481.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.092140 restraints weight = 15234.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092388 restraints weight = 14003.362| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29896 Z= 0.150 Angle : 0.582 9.002 40782 Z= 0.299 Chirality : 0.043 0.277 4757 Planarity : 0.004 0.091 5164 Dihedral : 14.483 155.143 4879 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 2.71 % Allowed : 19.48 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3767 helix: 0.81 (0.16), residues: 1205 sheet: -1.17 (0.26), residues: 392 loop : -1.90 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1034 TYR 0.021 0.001 TYR C1281 PHE 0.015 0.001 PHE C 57 TRP 0.033 0.001 TRP C1276 HIS 0.025 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00353 (29890) covalent geometry : angle 0.58162 (40782) hydrogen bonds : bond 0.04329 ( 1051) hydrogen bonds : angle 4.20404 ( 2913) metal coordination : bond 0.00490 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7987 (p90) REVERT: B 29 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 122 GLU cc_start: 0.8095 (mp0) cc_final: 0.7444 (mp0) REVERT: B 177 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.6656 (p90) REVERT: C 47 TYR cc_start: 0.1875 (m-80) cc_final: 0.0114 (m-80) REVERT: C 187 GLU cc_start: 0.8067 (tp30) cc_final: 0.7808 (tt0) REVERT: C 291 TYR cc_start: 0.8628 (t80) cc_final: 0.8208 (t80) REVERT: C 337 PHE cc_start: 0.8844 (t80) cc_final: 0.8458 (t80) REVERT: C 369 MET cc_start: 0.8109 (ppp) cc_final: 0.7501 (ttp) REVERT: C 429 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8548 (mpp) REVERT: C 447 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7816 (t-170) REVERT: C 488 MET cc_start: 0.8466 (mmm) cc_final: 0.8175 (mmm) REVERT: C 588 GLU cc_start: 0.8441 (pt0) cc_final: 0.8084 (pt0) REVERT: C 714 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.9125 (p) REVERT: C 1027 LYS cc_start: 0.9214 (ptmt) cc_final: 0.8840 (pttm) REVERT: C 1056 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8356 (m) REVERT: C 1164 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7437 (m-10) REVERT: C 1229 TYR cc_start: 0.8888 (m-80) cc_final: 0.8201 (m-80) REVERT: C 1243 MET cc_start: 0.8810 (tmm) cc_final: 0.8252 (tmm) REVERT: C 1268 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7961 (mm-40) REVERT: C 1273 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: D 245 LEU cc_start: 0.8654 (tp) cc_final: 0.8427 (mp) REVERT: D 330 MET cc_start: 0.7586 (ttt) cc_final: 0.7346 (ttt) REVERT: D 551 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.6929 (ptm-80) REVERT: D 897 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: D 960 LEU cc_start: 0.8670 (mm) cc_final: 0.8133 (tp) REVERT: D 1028 ILE cc_start: 0.8987 (mm) cc_final: 0.8724 (tp) REVERT: D 1370 MET cc_start: 0.8595 (tpp) cc_final: 0.8006 (tmm) outliers start: 74 outliers final: 57 residues processed: 275 average time/residue: 0.1694 time to fit residues: 77.4892 Evaluate side-chains 279 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 341 optimal weight: 50.0000 chunk 226 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 chunk 267 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 50.0000 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 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 = 0.4038 r_free = 0.4038 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086101 restraints weight = 60507.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089127 restraints weight = 31156.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091160 restraints weight = 20503.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092314 restraints weight = 15756.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093241 restraints weight = 13573.498| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29896 Z= 0.131 Angle : 0.569 9.031 40782 Z= 0.292 Chirality : 0.043 0.263 4757 Planarity : 0.004 0.091 5164 Dihedral : 14.415 156.101 4879 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.67 % Allowed : 19.59 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3767 helix: 0.88 (0.16), residues: 1212 sheet: -1.10 (0.26), residues: 393 loop : -1.86 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 191 TYR 0.016 0.001 TYR D 631 PHE 0.014 0.001 PHE C 57 TRP 0.036 0.001 TRP C1276 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00306 (29890) covalent geometry : angle 0.56877 (40782) hydrogen bonds : bond 0.04176 ( 1051) hydrogen bonds : angle 4.09752 ( 2913) metal coordination : bond 0.00329 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 229 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7798 (p90) REVERT: B 29 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7321 (mt-10) REVERT: B 177 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6527 (p90) REVERT: C 47 TYR cc_start: 0.1795 (m-80) cc_final: 0.0019 (m-80) REVERT: C 187 GLU cc_start: 0.8028 (tp30) cc_final: 0.7798 (tt0) REVERT: C 291 TYR cc_start: 0.8277 (t80) cc_final: 0.8022 (t80) REVERT: C 337 PHE cc_start: 0.8815 (t80) cc_final: 0.8470 (t80) REVERT: C 369 MET cc_start: 0.8165 (ppp) cc_final: 0.7523 (ttp) REVERT: C 429 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8482 (mpp) REVERT: C 447 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7748 (t-170) REVERT: C 488 MET cc_start: 0.8582 (mmm) cc_final: 0.8312 (mmm) REVERT: C 588 GLU cc_start: 0.8412 (pt0) cc_final: 0.8002 (pt0) REVERT: C 714 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9140 (p) REVERT: C 1034 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8394 (ttp80) REVERT: C 1056 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (m) REVERT: C 1107 MET cc_start: 0.8334 (tpt) cc_final: 0.7658 (tpt) REVERT: C 1164 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: C 1229 TYR cc_start: 0.8823 (m-80) cc_final: 0.8055 (m-80) REVERT: C 1232 MET cc_start: 0.8352 (ttm) cc_final: 0.8017 (ttm) REVERT: C 1268 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7793 (mm-40) REVERT: C 1273 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: C 1276 TRP cc_start: 0.8402 (m-10) cc_final: 0.8138 (m-90) REVERT: D 245 LEU cc_start: 0.8664 (tp) cc_final: 0.8443 (mp) REVERT: D 330 MET cc_start: 0.7423 (ttt) cc_final: 0.7194 (ttt) REVERT: D 551 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6968 (ptm-80) REVERT: D 897 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: D 960 LEU cc_start: 0.8653 (mm) cc_final: 0.8109 (tp) REVERT: D 1028 ILE cc_start: 0.8986 (mm) cc_final: 0.8754 (tp) REVERT: D 1123 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: D 1370 MET cc_start: 0.8573 (tpp) cc_final: 0.7991 (tmm) outliers start: 73 outliers final: 55 residues processed: 284 average time/residue: 0.1669 time to fit residues: 78.7152 Evaluate side-chains 286 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 44 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 359 optimal weight: 50.0000 chunk 230 optimal weight: 0.9980 chunk 142 optimal weight: 0.0060 chunk 288 optimal weight: 10.0000 chunk 362 optimal weight: 50.0000 chunk 120 optimal weight: 0.0170 chunk 82 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 overall best weight: 2.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 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 = 0.4016 r_free = 0.4016 target = 0.137526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085667 restraints weight = 61147.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090013 restraints weight = 34194.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090286 restraints weight = 20700.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091234 restraints weight = 15424.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091494 restraints weight = 14131.563| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29896 Z= 0.191 Angle : 0.609 8.977 40782 Z= 0.312 Chirality : 0.044 0.264 4757 Planarity : 0.005 0.091 5164 Dihedral : 14.453 155.296 4879 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 2.78 % Allowed : 19.77 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3767 helix: 0.85 (0.16), residues: 1210 sheet: -1.05 (0.26), residues: 385 loop : -1.90 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1148 TYR 0.020 0.001 TYR C1281 PHE 0.014 0.001 PHE D 17 TRP 0.037 0.002 TRP C1276 HIS 0.005 0.001 HIS C1313 Details of bonding type rmsd covalent geometry : bond 0.00453 (29890) covalent geometry : angle 0.60940 (40782) hydrogen bonds : bond 0.04488 ( 1051) hydrogen bonds : angle 4.18820 ( 2913) metal coordination : bond 0.00554 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5204.67 seconds wall clock time: 90 minutes 39.59 seconds (5439.59 seconds total)