Starting phenix.real_space_refine on Sat Mar 7 02:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pga_71624/03_2026/9pga_71624.map" } resolution = 3.98 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= 0.000 sd= 0.030 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 121 5.49 5 Mg 1 5.21 5 S 123 5.16 5 C 22075 2.51 5 N 6405 2.21 5 O 6990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s 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: 35717 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1710 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 14, 'TRANS': 216} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2361 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 10222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1346, 10222 Classifications: {'peptide': 1346} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 64, 'TRANS': 1281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 12, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 18, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 10027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10027 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1270} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 17, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 212 Chain: "E" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 495 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3485 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 11, 'TRANS': 462} Chain breaks: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 14, 'ASP:plan': 7, 'PHE:plan': 4, 'TYR:plan': 3, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 206 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1312 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "I" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1044 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "Q" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2474 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 309} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "R" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2462 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 306} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 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 14748 SG CYS D 71 111.304 104.029 74.850 1.00127.79 S ATOM 14762 SG CYS D 73 115.080 101.443 74.486 1.00124.51 S ATOM 20460 SG CYS D 810 45.505 101.967 90.205 1.00 79.43 S ATOM 20990 SG CYS D 884 47.459 99.170 92.169 1.00 76.75 S ATOM 21038 SG CYS D 891 48.330 102.888 92.618 1.00 77.80 S ATOM 21053 SG CYS D 894 45.308 101.497 93.982 1.00 67.69 S Time building chain proxies: 7.22, per 1000 atoms: 0.20 Number of scatterers: 35717 At special positions: 0 Unit cell: (205.2, 167.4, 183.6, 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 123 16.00 P 121 15.00 Mg 1 11.99 O 6990 8.00 N 6405 7.00 C 22075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 810 " Number of angles added : 6 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 48 sheets defined 41.7% alpha, 10.5% beta 23 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.533A pdb=" N ARG A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.677A pdb=" N LEU B 9 " --> pdb=" O TRP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.604A pdb=" N LEU B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 245 removed outlier: 4.174A pdb=" N LYS B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.579A pdb=" N ARG B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 312 removed outlier: 3.861A pdb=" N LEU B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.796A pdb=" N GLU C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 37' Processing helix chain 'C' and resid 52 through 61 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.879A pdb=" N ALA C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.622A pdb=" N THR C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.669A pdb=" N LYS C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.229A pdb=" N GLY C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.768A pdb=" N ILE C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.131A pdb=" N THR C 358 " --> pdb=" O TYR C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 406 through 417 Processing helix chain 'C' and resid 429 through 445 removed outlier: 4.133A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.784A pdb=" N ARG C 459 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 490 removed outlier: 4.097A pdb=" N LEU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 490 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.589A pdb=" N VAL C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 Processing helix chain 'C' and resid 548 through 552 removed outlier: 4.289A pdb=" N GLY C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.613A pdb=" N LYS C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 removed outlier: 4.113A pdb=" N VAL C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 675 Processing helix chain 'C' and resid 682 through 693 removed outlier: 3.919A pdb=" N MET C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 696 No H-bonds generated for 'chain 'C' and resid 694 through 696' Processing helix chain 'C' and resid 710 through 713 removed outlier: 3.740A pdb=" N ALA C 713 " --> pdb=" O GLY C 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 710 through 713' Processing helix chain 'C' and resid 714 through 719 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 826 through 832 Processing helix chain 'C' and resid 902 through 913 Processing helix chain 'C' and resid 948 through 982 Processing helix chain 'C' and resid 1004 through 1009 removed outlier: 3.666A pdb=" N GLN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1016 removed outlier: 3.912A pdb=" N TRP C1016 " --> pdb=" O SER C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1056 removed outlier: 4.296A pdb=" N SER C1031 " --> pdb=" O GLY C1027 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1124 removed outlier: 4.589A pdb=" N SER C1123 " --> pdb=" O LEU C1119 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C1124 " --> pdb=" O GLY C1120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1119 through 1124' Processing helix chain 'C' and resid 1127 through 1153 removed outlier: 3.625A pdb=" N PHE C1131 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP C1153 " --> pdb=" O LEU C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1170 Processing helix chain 'C' and resid 1179 through 1190 Processing helix chain 'C' and resid 1191 through 1193 No H-bonds generated for 'chain 'C' and resid 1191 through 1193' Processing helix chain 'C' and resid 1205 through 1217 Processing helix chain 'C' and resid 1285 through 1295 removed outlier: 3.715A pdb=" N TYR C1295 " --> pdb=" O ALA C1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1306 Processing helix chain 'C' and resid 1314 through 1325 Processing helix chain 'C' and resid 1334 through 1346 removed outlier: 3.620A pdb=" N ASN C1338 " --> pdb=" O PRO C1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.967A pdb=" N GLY D 74 " --> pdb=" O CYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.525A pdb=" N VAL D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 3.690A pdb=" N SER D 120 " --> pdb=" O TRP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.844A pdb=" N ALA D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.907A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 3.760A pdb=" N TRP D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.841A pdb=" N ASP D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 removed outlier: 3.761A pdb=" N ASP D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 344 removed outlier: 3.738A pdb=" N ASN D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 379 through 391 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 409 through 418 removed outlier: 4.086A pdb=" N ILE D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 454 No H-bonds generated for 'chain 'D' and resid 452 through 454' Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 531 through 542 removed outlier: 3.798A pdb=" N ILE D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.640A pdb=" N LEU D 591 " --> pdb=" O GLY D 588 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 592 " --> pdb=" O HIS D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.534A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 Processing helix chain 'D' and resid 674 through 685 Processing helix chain 'D' and resid 685 through 701 Processing helix chain 'D' and resid 716 through 725 removed outlier: 3.603A pdb=" N SER D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 725 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 738 Processing helix chain 'D' and resid 764 through 800 removed outlier: 3.841A pdb=" N GLY D 774 " --> pdb=" O ASN D 770 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 836 Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.571A pdb=" N ALA D 865 " --> pdb=" O ASP D 861 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1128 through 1138 Processing helix chain 'D' and resid 1212 through 1220 removed outlier: 3.920A pdb=" N ARG D1218 " --> pdb=" O HIS D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1240 removed outlier: 3.707A pdb=" N VAL D1236 " --> pdb=" O GLU D1232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D1237 " --> pdb=" O ILE D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1246 through 1257 Processing helix chain 'D' and resid 1278 through 1292 removed outlier: 3.798A pdb=" N ARG D1291 " --> pdb=" O LYS D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1311 Processing helix chain 'D' and resid 1315 through 1322 Processing helix chain 'D' and resid 1323 through 1335 removed outlier: 4.089A pdb=" N VAL D1327 " --> pdb=" O GLU D1323 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D1329 " --> pdb=" O THR D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1342 through 1349 removed outlier: 3.782A pdb=" N ASN D1346 " --> pdb=" O GLY D1342 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1375 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 30 removed outlier: 4.507A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 44 through 54 removed outlier: 4.001A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 66 removed outlier: 3.812A pdb=" N LYS E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 126 removed outlier: 3.863A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER F 124 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 149 Processing helix chain 'F' and resid 157 through 166 removed outlier: 4.008A pdb=" N VAL F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TRP F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 259 removed outlier: 3.647A pdb=" N SER F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.881A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 298 removed outlier: 3.937A pdb=" N ARG F 282 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR F 298 " --> pdb=" O GLN F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 333 removed outlier: 3.564A pdb=" N ILE F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 347 removed outlier: 4.067A pdb=" N GLY F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 356 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 368 through 391 removed outlier: 3.861A pdb=" N GLN F 374 " --> pdb=" O GLU F 370 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 422 removed outlier: 3.560A pdb=" N LYS F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 430 removed outlier: 4.381A pdb=" N VAL F 426 " --> pdb=" O ASN F 422 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE F 427 " --> pdb=" O LEU F 423 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 455 Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 465 through 485 removed outlier: 3.866A pdb=" N TYR F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP F 472 " --> pdb=" O THR F 468 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP F 473 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 510 removed outlier: 4.512A pdb=" N THR F 498 " --> pdb=" O HIS F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 526 removed outlier: 4.631A pdb=" N GLU F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 removed outlier: 3.689A pdb=" N LEU F 537 " --> pdb=" O VAL F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.576A pdb=" N PHE F 561 " --> pdb=" O LEU F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 588 removed outlier: 3.746A pdb=" N ALA F 588 " --> pdb=" O THR F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 602 Processing helix chain 'F' and resid 611 through 620 removed outlier: 3.543A pdb=" N SER F 620 " --> pdb=" O GLY F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 638 Processing helix chain 'F' and resid 643 through 648 removed outlier: 4.358A pdb=" N SER F 648 " --> pdb=" O ARG F 644 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 20 removed outlier: 3.707A pdb=" N ALA Q 6 " --> pdb=" O ARG Q 2 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR Q 7 " --> pdb=" O HIS Q 3 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 32 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 78 through 96 removed outlier: 4.025A pdb=" N ALA Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Q 86 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 114 removed outlier: 4.157A pdb=" N LEU Q 104 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU Q 108 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 124 removed outlier: 3.847A pdb=" N ARG Q 121 " --> pdb=" O GLY Q 117 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG Q 122 " --> pdb=" O SER Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 Processing helix chain 'Q' and resid 147 through 159 Processing helix chain 'Q' and resid 228 through 236 removed outlier: 4.138A pdb=" N SER Q 236 " --> pdb=" O PHE Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 256 through 260 Processing helix chain 'Q' and resid 286 through 298 removed outlier: 4.443A pdb=" N TRP Q 292 " --> pdb=" O ARG Q 288 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS Q 293 " --> pdb=" O GLU Q 289 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR Q 296 " --> pdb=" O TRP Q 292 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP Q 297 " --> pdb=" O HIS Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 325 removed outlier: 3.763A pdb=" N LYS Q 310 " --> pdb=" O PRO Q 306 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP Q 311 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET Q 312 " --> pdb=" O VAL Q 308 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET Q 313 " --> pdb=" O LEU Q 309 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL Q 314 " --> pdb=" O LYS Q 310 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN Q 315 " --> pdb=" O ASP Q 311 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU Q 316 " --> pdb=" O MET Q 312 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS Q 324 " --> pdb=" O ALA Q 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 18 removed outlier: 3.980A pdb=" N LEU R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.231A pdb=" N MET R 28 " --> pdb=" O THR R 24 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 50 removed outlier: 3.669A pdb=" N GLU R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 94 removed outlier: 4.045A pdb=" N LEU R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 114 Processing helix chain 'R' and resid 116 through 123 Processing helix chain 'R' and resid 123 through 132 removed outlier: 3.899A pdb=" N VAL R 127 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 161 removed outlier: 3.915A pdb=" N ALA R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 211 No H-bonds generated for 'chain 'R' and resid 209 through 211' Processing helix chain 'R' and resid 228 through 236 removed outlier: 3.873A pdb=" N SER R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 261 Processing helix chain 'R' and resid 286 through 296 removed outlier: 4.274A pdb=" N THR R 296 " --> pdb=" O TRP R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 324 removed outlier: 3.813A pdb=" N LYS R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 314 " --> pdb=" O LYS R 310 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG R 318 " --> pdb=" O VAL R 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.824A pdb=" N ALA A 27 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 204 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 201 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 184 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 203 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 182 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 205 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 6.471A pdb=" N ASN A 149 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 59 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY A 151 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA A 57 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.921A pdb=" N VAL A 155 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.989A pdb=" N ARG B 28 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.732A pdb=" N GLU B 145 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE B 62 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 60 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 170 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.693A pdb=" N VAL B 113 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N CYS B 134 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.443A pdb=" N LYS C 13 " --> pdb=" O ALA C1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.839A pdb=" N ILE C 63 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA C 98 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 132 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 100 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 164 removed outlier: 3.786A pdb=" N ILE C 204 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 237 Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AB7, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB8, first strand: chain 'C' and resid 611 through 614 Processing sheet with id=AB9, first strand: chain 'C' and resid 624 through 625 Processing sheet with id=AC1, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.117A pdb=" N GLN C 733 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 774 through 775 removed outlier: 3.539A pdb=" N ASP C 791 " --> pdb=" O ARG C 774 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 795 through 796 Processing sheet with id=AC4, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 6.718A pdb=" N ILE C 822 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE C1097 " --> pdb=" O ILE C 822 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 824 " --> pdb=" O ILE C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 823 " --> pdb=" O VAL C1115 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N VAL C1114 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU C 807 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C1116 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA C 809 " --> pdb=" O LEU C1116 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C1240 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 836 through 845 removed outlier: 6.670A pdb=" N MET C1067 " --> pdb=" O VAL C 939 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL C 939 " --> pdb=" O MET C1067 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS C1069 " --> pdb=" O VAL C 937 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 937 " --> pdb=" O LYS C1069 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE C1071 " --> pdb=" O VAL C 935 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C1073 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 888 through 890 Processing sheet with id=AC7, first strand: chain 'C' and resid 893 through 895 Processing sheet with id=AC8, first strand: chain 'C' and resid 990 through 992 removed outlier: 6.946A pdb=" N ALA C1019 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 112 removed outlier: 3.676A pdb=" N LEU D 108 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR D 242 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AD3, first strand: chain 'D' and resid 263 through 264 Processing sheet with id=AD4, first strand: chain 'D' and resid 436 through 439 Processing sheet with id=AD5, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.105A pdb=" N CYS D 368 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 444 " --> pdb=" O CYS D 368 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 370 " --> pdb=" O ILE D 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 528 through 529 removed outlier: 3.715A pdb=" N ARG D 553 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 805 through 807 removed outlier: 7.437A pdb=" N VAL D 890 " --> pdb=" O VAL D 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 816 through 818 Processing sheet with id=AD9, first strand: chain 'D' and resid 952 through 956 Processing sheet with id=AE1, first strand: chain 'D' and resid 959 through 961 removed outlier: 3.868A pdb=" N LEU D 967 " --> pdb=" O LEU D 996 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 4.370A pdb=" N ALA D1113 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1090 through 1091 Processing sheet with id=AE4, first strand: chain 'D' and resid 1039 through 1043 Processing sheet with id=AE5, first strand: chain 'D' and resid 1167 through 1169 removed outlier: 3.624A pdb=" N GLY D1152 " --> pdb=" O ILE D1200 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 6.764A pdb=" N VAL D1297 " --> pdb=" O LEU D1263 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 134 through 135 removed outlier: 7.847A pdb=" N THR Q 135 " --> pdb=" O PHE R 187 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 134 through 135 removed outlier: 7.847A pdb=" N THR Q 135 " --> pdb=" O PHE R 187 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU R 196 " --> pdb=" O PRO R 182 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 193 " --> pdb=" O TRP R 206 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 195 " --> pdb=" O ARG R 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 204 " --> pdb=" O ALA R 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 204 through 207 removed outlier: 3.602A pdb=" N VAL Q 194 " --> pdb=" O GLY Q 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY Q 184 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU Q 196 " --> pdb=" O PRO Q 182 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLN Q 162 " --> pdb=" O PRO Q 182 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 269 through 272 removed outlier: 8.291A pdb=" N VAL Q 248 " --> pdb=" O VAL Q 304 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL Q 304 " --> pdb=" O VAL Q 248 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 54 through 56 Processing sheet with id=AF3, first strand: chain 'R' and resid 271 through 272 removed outlier: 3.807A pdb=" N THR R 271 " --> pdb=" O LEU R 279 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU R 279 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 305 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG R 250 " --> pdb=" O ILE R 303 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE R 303 " --> pdb=" O ARG R 250 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 9.02 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10972 1.33 - 1.46: 5829 1.46 - 1.58: 19272 1.58 - 1.70: 238 1.70 - 1.82: 224 Bond restraints: 36535 Sorted by residual: bond pdb=" O3' DA H 1 " pdb=" P DT H 2 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.60e+00 bond pdb=" CB PRO C 885 " pdb=" CG PRO C 885 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.55e+00 bond pdb=" CB PRO C 505 " pdb=" CG PRO C 505 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CG ARG R 100 " pdb=" CD ARG R 100 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" C VAL D1106 " pdb=" N LYS D1107 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.48e-02 4.57e+03 1.87e+00 ... (remaining 36530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 49180 2.23 - 4.45: 726 4.45 - 6.68: 90 6.68 - 8.90: 16 8.90 - 11.13: 4 Bond angle restraints: 50016 Sorted by residual: angle pdb=" CA PRO C 505 " pdb=" N PRO C 505 " pdb=" CD PRO C 505 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N ILE D 864 " pdb=" CA ILE D 864 " pdb=" C ILE D 864 " ideal model delta sigma weight residual 111.81 107.94 3.87 8.60e-01 1.35e+00 2.02e+01 angle pdb=" CG ARG R 100 " pdb=" CD ARG R 100 " pdb=" NE ARG R 100 " ideal model delta sigma weight residual 112.00 120.53 -8.53 2.20e+00 2.07e-01 1.50e+01 angle pdb=" N ILE F 604 " pdb=" CA ILE F 604 " pdb=" C ILE F 604 " ideal model delta sigma weight residual 111.62 108.56 3.06 7.90e-01 1.60e+00 1.50e+01 angle pdb=" N LEU F 323 " pdb=" CA LEU F 323 " pdb=" C LEU F 323 " ideal model delta sigma weight residual 113.43 108.68 4.75 1.26e+00 6.30e-01 1.42e+01 ... (remaining 50011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 21091 35.37 - 70.74: 783 70.74 - 106.10: 33 106.10 - 141.47: 1 141.47 - 176.84: 4 Dihedral angle restraints: 21912 sinusoidal: 9278 harmonic: 12634 Sorted by residual: dihedral pdb=" CA LYS C 504 " pdb=" C LYS C 504 " pdb=" N PRO C 505 " pdb=" CA PRO C 505 " ideal model delta harmonic sigma weight residual 180.00 149.39 30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLY C1089 " pdb=" C GLY C1089 " pdb=" N ASN C1090 " pdb=" CA ASN C1090 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA VAL D 881 " pdb=" C VAL D 881 " pdb=" N LEU D 882 " pdb=" CA LEU D 882 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 21909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3918 0.038 - 0.075: 1313 0.075 - 0.113: 456 0.113 - 0.150: 90 0.150 - 0.188: 6 Chirality restraints: 5783 Sorted by residual: chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE C 199 " pdb=" N ILE C 199 " pdb=" C ILE C 199 " pdb=" CB ILE C 199 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" P DT H 2 " pdb=" OP1 DT H 2 " pdb=" OP2 DT H 2 " pdb=" O5' DT H 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 5780 not shown) Planarity restraints: 6142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 219 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO Q 220 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO Q 220 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO Q 220 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 319 " -0.383 9.50e-02 1.11e+02 1.72e-01 1.81e+01 pdb=" NE ARG F 319 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 319 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 319 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 319 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1034 " -0.340 9.50e-02 1.11e+02 1.52e-01 1.44e+01 pdb=" NE ARG C1034 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C1034 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C1034 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C1034 " -0.010 2.00e-02 2.50e+03 ... (remaining 6139 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 227 2.51 - 3.11: 26743 3.11 - 3.70: 54691 3.70 - 4.30: 71474 4.30 - 4.90: 114736 Nonbonded interactions: 267871 Sorted by model distance: nonbonded pdb=" OD2 ASP D 466 " pdb="MG MG D2001 " model vdw 1.911 2.170 nonbonded pdb=" NH1 ARG F 271 " pdb=" O GLU F 349 " model vdw 1.951 3.120 nonbonded pdb=" OG SER D 880 " pdb=" OE1 GLU D1250 " model vdw 2.091 3.040 nonbonded pdb=" O MET D 721 " pdb=" OG SER D 724 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 60 " pdb=" ND2 ASN A 160 " model vdw 2.131 3.120 ... (remaining 267866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'Y' } ncs_group { reference = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 92 or (resid 93 through 94 and (name N or name CA \ or name C or name O or name CB )) or resid 95 through 161 or (resid 162 through \ 163 and (name N or name CA or name C or name O or name CB )) or resid 164 throu \ gh 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) or \ resid 228 through 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 327)) selection = (chain 'R' and (resid 4 through 62 or (resid 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 103 or (resid 104 and \ (name N or name CA or name C or name O or name CB )) or resid 105 through 115 or \ (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 124 or (resid 125 and (name N or name CA or name C or name O or name C \ B )) or resid 126 through 138 or (resid 139 through 140 and (name N or name CA o \ r name C or name O or name CB )) or resid 141 through 175 or (resid 176 and (nam \ e N or name CA or name C or name O or name CB )) or resid 177 through 223 or (re \ sid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 th \ rough 310 or (resid 311 and (name N or name CA or name C or name O or name CB )) \ or resid 312 through 315 or (resid 316 and (name N or name CA or name C or name \ O or name CB )) or resid 317 through 327)) } 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 39.380 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 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 : 0.004 0.094 36541 Z= 0.176 Angle : 0.679 11.130 50022 Z= 0.354 Chirality : 0.043 0.188 5783 Planarity : 0.006 0.172 6142 Dihedral : 16.937 176.841 13764 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.55 (0.13), residues: 4397 helix: 0.20 (0.13), residues: 1607 sheet: -0.65 (0.25), residues: 422 loop : -2.06 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 120 TYR 0.033 0.002 TYR C 472 PHE 0.019 0.002 PHE D 439 TRP 0.043 0.002 TRP D 34 HIS 0.008 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00393 (36535) covalent geometry : angle 0.67665 (50016) hydrogen bonds : bond 0.16293 ( 1390) hydrogen bonds : angle 6.52316 ( 3876) metal coordination : bond 0.01286 ( 6) metal coordination : angle 4.66715 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLU cc_start: 0.7152 (pm20) cc_final: 0.6873 (pm20) REVERT: C 438 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8189 (mmtp) REVERT: C 532 ILE cc_start: 0.8782 (tp) cc_final: 0.8556 (tp) REVERT: C 629 ILE cc_start: 0.8689 (mm) cc_final: 0.8388 (tp) REVERT: C 640 LEU cc_start: 0.8671 (mm) cc_final: 0.8380 (mm) REVERT: C 692 MET cc_start: 0.7332 (mtm) cc_final: 0.7108 (mtm) REVERT: C 814 ASN cc_start: 0.8005 (t0) cc_final: 0.7751 (t0) REVERT: C 901 MET cc_start: 0.5909 (mmm) cc_final: 0.4537 (mtt) REVERT: D 392 LEU cc_start: 0.5875 (mm) cc_final: 0.5669 (mm) REVERT: D 539 MET cc_start: 0.6870 (tpt) cc_final: 0.6658 (tpt) REVERT: D 1150 MET cc_start: 0.7342 (tmm) cc_final: 0.7111 (tmm) REVERT: F 526 LEU cc_start: 0.8867 (mm) cc_final: 0.8593 (mm) REVERT: F 606 MET cc_start: 0.4537 (mpp) cc_final: 0.4256 (mpp) REVERT: Q 244 ILE cc_start: 0.7011 (mp) cc_final: 0.6803 (mp) REVERT: Q 283 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7988 (mtp85) REVERT: R 287 MET cc_start: 0.5068 (mmm) cc_final: 0.4763 (mmp) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.2309 time to fit residues: 215.4150 Evaluate side-chains 537 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 160 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 976 ASN ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1302 GLN D 268 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 GLN ** Q 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.256929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.177864 restraints weight = 40767.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.180729 restraints weight = 25315.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186284 restraints weight = 16277.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.189636 restraints weight = 10008.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.189860 restraints weight = 8043.254| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36541 Z= 0.160 Angle : 0.651 10.822 50022 Z= 0.335 Chirality : 0.043 0.218 5783 Planarity : 0.005 0.084 6142 Dihedral : 16.160 179.759 6081 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.64 % Allowed : 11.63 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4397 helix: 0.30 (0.13), residues: 1660 sheet: -0.69 (0.25), residues: 420 loop : -2.11 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 271 TYR 0.026 0.002 TYR C 472 PHE 0.019 0.001 PHE C 513 TRP 0.028 0.001 TRP D 34 HIS 0.007 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00360 (36535) covalent geometry : angle 0.64918 (50016) hydrogen bonds : bond 0.04653 ( 1390) hydrogen bonds : angle 5.15314 ( 3876) metal coordination : bond 0.01106 ( 6) metal coordination : angle 4.13977 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 554 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 ARG cc_start: 0.7482 (tpt90) cc_final: 0.7081 (tpt90) REVERT: B 51 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 80 ASP cc_start: 0.8841 (t0) cc_final: 0.8487 (t0) REVERT: B 102 ARG cc_start: 0.7368 (mmp80) cc_final: 0.7135 (mmp80) REVERT: C 532 ILE cc_start: 0.8536 (tp) cc_final: 0.8226 (tp) REVERT: C 692 MET cc_start: 0.7637 (mtm) cc_final: 0.7179 (mtm) REVERT: C 901 MET cc_start: 0.6108 (mmm) cc_final: 0.4544 (mtt) REVERT: C 920 ARG cc_start: 0.6850 (ptt180) cc_final: 0.6230 (tmm-80) REVERT: C 1260 ARG cc_start: 0.8058 (ttt-90) cc_final: 0.7289 (ttt-90) REVERT: C 1287 MET cc_start: 0.6225 (pmm) cc_final: 0.5197 (mmt) REVERT: D 239 MET cc_start: 0.6793 (ttt) cc_final: 0.6240 (tpt) REVERT: D 730 GLN cc_start: 0.7826 (mt0) cc_final: 0.7184 (tp40) REVERT: D 1143 ASP cc_start: 0.6620 (p0) cc_final: 0.6253 (p0) REVERT: D 1150 MET cc_start: 0.6911 (tmm) cc_final: 0.6362 (tmm) REVERT: E 7 GLU cc_start: 0.7976 (mp0) cc_final: 0.7689 (mp0) REVERT: Q 86 ARG cc_start: 0.7889 (tpm170) cc_final: 0.7672 (tpm170) REVERT: Q 244 ILE cc_start: 0.6766 (mp) cc_final: 0.5668 (mp) REVERT: R 42 MET cc_start: 0.8892 (mmt) cc_final: 0.8494 (mmt) outliers start: 55 outliers final: 41 residues processed: 578 average time/residue: 0.2356 time to fit residues: 215.4218 Evaluate side-chains 560 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 518 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 304 optimal weight: 8.9990 chunk 420 optimal weight: 1.9990 chunk 437 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 335 optimal weight: 3.9990 chunk 169 optimal weight: 0.0050 chunk 120 optimal weight: 3.9990 overall best weight: 0.8896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1278 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 GLN ** R 293 HIS ** 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 = 0.4926 r_free = 0.4926 target = 0.254297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.178395 restraints weight = 40214.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182483 restraints weight = 24394.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.186782 restraints weight = 14008.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.189130 restraints weight = 9462.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.191282 restraints weight = 7792.615| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36541 Z= 0.152 Angle : 0.626 10.519 50022 Z= 0.321 Chirality : 0.042 0.192 5783 Planarity : 0.005 0.063 6142 Dihedral : 16.153 179.756 6081 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.54 % Allowed : 15.81 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4397 helix: 0.34 (0.13), residues: 1665 sheet: -0.58 (0.26), residues: 406 loop : -2.11 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1345 TYR 0.025 0.002 TYR C 472 PHE 0.019 0.001 PHE R 295 TRP 0.025 0.001 TRP D 34 HIS 0.007 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00344 (36535) covalent geometry : angle 0.62321 (50016) hydrogen bonds : bond 0.04173 ( 1390) hydrogen bonds : angle 4.91917 ( 3876) metal coordination : bond 0.01309 ( 6) metal coordination : angle 5.82029 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 549 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7272 (mmm-85) cc_final: 0.6952 (mmm-85) REVERT: B 4 ARG cc_start: 0.7459 (tpt90) cc_final: 0.7024 (tpt90) REVERT: B 51 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 80 ASP cc_start: 0.8785 (t0) cc_final: 0.8492 (t0) REVERT: C 356 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7225 (tmm160) REVERT: C 532 ILE cc_start: 0.8559 (tp) cc_final: 0.8236 (tp) REVERT: C 660 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.5046 (ppp) REVERT: C 692 MET cc_start: 0.7600 (mtm) cc_final: 0.7152 (mtm) REVERT: C 901 MET cc_start: 0.6171 (mmm) cc_final: 0.4521 (mtt) REVERT: C 920 ARG cc_start: 0.6961 (ptt180) cc_final: 0.6597 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6594 (p-80) REVERT: C 1260 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7202 (ttt-90) REVERT: C 1287 MET cc_start: 0.6237 (pmm) cc_final: 0.5326 (mmt) REVERT: D 116 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: D 125 ILE cc_start: 0.4618 (OUTLIER) cc_final: 0.4365 (tp) REVERT: D 127 MET cc_start: 0.7262 (tpp) cc_final: 0.7061 (tpp) REVERT: D 238 TRP cc_start: 0.7294 (m-90) cc_final: 0.6386 (m-90) REVERT: D 239 MET cc_start: 0.6862 (ttt) cc_final: 0.6343 (tpt) REVERT: D 288 ARG cc_start: 0.8226 (ptp-110) cc_final: 0.7947 (mtp85) REVERT: D 401 ARG cc_start: 0.8014 (ptt90) cc_final: 0.7618 (ptm-80) REVERT: D 550 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 720 MET cc_start: 0.7165 (mmm) cc_final: 0.6945 (mmm) REVERT: D 730 GLN cc_start: 0.7665 (mt0) cc_final: 0.7137 (tp40) REVERT: D 1143 ASP cc_start: 0.6750 (p0) cc_final: 0.6221 (p0) REVERT: D 1150 MET cc_start: 0.6772 (tmm) cc_final: 0.6050 (tmm) REVERT: D 1155 GLU cc_start: 0.7956 (pt0) cc_final: 0.7653 (pp20) REVERT: Q 261 ARG cc_start: 0.7280 (mmp80) cc_final: 0.6906 (ptt-90) REVERT: R 42 MET cc_start: 0.8920 (mmt) cc_final: 0.8501 (mmt) outliers start: 85 outliers final: 56 residues processed: 588 average time/residue: 0.2208 time to fit residues: 206.9607 Evaluate side-chains 582 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 520 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 196 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 403 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 374 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 446 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1278 GLN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 GLN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN Q 225 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.244610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171049 restraints weight = 40727.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.172630 restraints weight = 24336.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176252 restraints weight = 15406.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179626 restraints weight = 10360.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180005 restraints weight = 7935.455| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 36541 Z= 0.278 Angle : 0.797 14.079 50022 Z= 0.413 Chirality : 0.047 0.226 5783 Planarity : 0.006 0.063 6142 Dihedral : 16.420 179.923 6081 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 5.19 % Allowed : 18.71 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.96 (0.12), residues: 4397 helix: -0.09 (0.13), residues: 1660 sheet: -0.76 (0.25), residues: 422 loop : -2.41 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 149 TYR 0.037 0.003 TYR C 472 PHE 0.024 0.002 PHE D 439 TRP 0.032 0.002 TRP D 34 HIS 0.012 0.002 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00622 (36535) covalent geometry : angle 0.79091 (50016) hydrogen bonds : bond 0.05125 ( 1390) hydrogen bonds : angle 5.45134 ( 3876) metal coordination : bond 0.02030 ( 6) metal coordination : angle 9.02591 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 540 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6360 (mmm-85) REVERT: B 4 ARG cc_start: 0.7560 (tpt90) cc_final: 0.7018 (tpt90) REVERT: C 230 PHE cc_start: 0.8225 (m-80) cc_final: 0.7781 (m-10) REVERT: C 356 ARG cc_start: 0.7528 (tmt170) cc_final: 0.7236 (tmm160) REVERT: C 416 ARG cc_start: 0.7442 (tpt170) cc_final: 0.7236 (tpt170) REVERT: C 614 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7235 (mmm) REVERT: C 660 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4953 (ppp) REVERT: C 692 MET cc_start: 0.7563 (mtm) cc_final: 0.7218 (mtm) REVERT: C 701 GLN cc_start: 0.7603 (tt0) cc_final: 0.7006 (tm-30) REVERT: C 732 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 817 ASN cc_start: 0.7771 (p0) cc_final: 0.7545 (p0) REVERT: C 901 MET cc_start: 0.6980 (mmm) cc_final: 0.5250 (mtt) REVERT: C 926 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6100 (tt) REVERT: C 1066 LYS cc_start: 0.7733 (ptmm) cc_final: 0.7483 (ptmm) REVERT: C 1118 PRO cc_start: 0.7983 (Cg_endo) cc_final: 0.7530 (Cg_exo) REVERT: C 1251 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.6761 (p-80) REVERT: C 1287 MET cc_start: 0.6725 (pmm) cc_final: 0.5928 (mmt) REVERT: D 116 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6681 (m-10) REVERT: D 239 MET cc_start: 0.6996 (ttt) cc_final: 0.6409 (tpt) REVERT: D 310 ASP cc_start: 0.8483 (t0) cc_final: 0.8133 (t0) REVERT: D 421 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5762 (t70) REVERT: D 487 MET cc_start: 0.6841 (mmm) cc_final: 0.6606 (mmm) REVERT: D 525 GLU cc_start: 0.7202 (tt0) cc_final: 0.6543 (pm20) REVERT: D 550 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 720 MET cc_start: 0.7311 (mmm) cc_final: 0.6915 (mmm) REVERT: D 730 GLN cc_start: 0.7806 (mt0) cc_final: 0.7185 (tp40) REVERT: D 1143 ASP cc_start: 0.7095 (p0) cc_final: 0.6543 (p0) REVERT: D 1150 MET cc_start: 0.7221 (tmm) cc_final: 0.6163 (tmm) REVERT: F 606 MET cc_start: 0.3687 (mpt) cc_final: 0.3463 (mpt) REVERT: Q 53 MET cc_start: 0.6995 (mmm) cc_final: 0.6778 (mmm) REVERT: Q 261 ARG cc_start: 0.7425 (mmp80) cc_final: 0.6974 (ptt-90) REVERT: R 42 MET cc_start: 0.8906 (mmt) cc_final: 0.8416 (mmt) REVERT: R 74 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6391 (m-10) outliers start: 174 outliers final: 115 residues processed: 646 average time/residue: 0.2188 time to fit residues: 227.7926 Evaluate side-chains 640 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 517 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 926 LEU Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1146 VAL Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1204 GLU Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 482 ILE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain R residue 15 MET Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 151 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 413 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 216 optimal weight: 0.2980 chunk 248 optimal weight: 0.9990 chunk 321 optimal weight: 0.8980 chunk 404 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 628 ASN ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1271 GLN C1278 GLN C1302 GLN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 702 GLN D 723 HIS ** F 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.250861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.175654 restraints weight = 40352.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.177801 restraints weight = 24389.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.183245 restraints weight = 15652.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186058 restraints weight = 9831.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186738 restraints weight = 8087.386| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36541 Z= 0.144 Angle : 0.644 11.641 50022 Z= 0.329 Chirality : 0.043 0.275 5783 Planarity : 0.004 0.061 6142 Dihedral : 16.291 179.700 6081 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.88 % Allowed : 22.29 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.60 (0.12), residues: 4397 helix: 0.27 (0.13), residues: 1663 sheet: -0.64 (0.26), residues: 386 loop : -2.22 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 100 TYR 0.018 0.002 TYR D 719 PHE 0.028 0.001 PHE R 295 TRP 0.020 0.001 TRP D 34 HIS 0.006 0.001 HIS D1214 Details of bonding type rmsd covalent geometry : bond 0.00325 (36535) covalent geometry : angle 0.64088 (50016) hydrogen bonds : bond 0.04108 ( 1390) hydrogen bonds : angle 4.89969 ( 3876) metal coordination : bond 0.01322 ( 6) metal coordination : angle 6.22185 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 539 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6702 (mmm-85) REVERT: A 125 GLU cc_start: 0.8405 (tp30) cc_final: 0.8083 (tp30) REVERT: B 4 ARG cc_start: 0.7494 (tpt90) cc_final: 0.6951 (tpt90) REVERT: B 102 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8060 (tpp80) REVERT: B 125 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 200 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3426 (mt) REVERT: C 230 PHE cc_start: 0.8067 (m-80) cc_final: 0.7600 (m-10) REVERT: C 640 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (mm) REVERT: C 660 MET cc_start: 0.5062 (OUTLIER) cc_final: 0.4786 (ppp) REVERT: C 692 MET cc_start: 0.7496 (mtm) cc_final: 0.7148 (mtm) REVERT: C 732 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 759 MET cc_start: 0.8147 (mmt) cc_final: 0.7889 (mmt) REVERT: C 817 ASN cc_start: 0.7403 (p0) cc_final: 0.6981 (p0) REVERT: C 901 MET cc_start: 0.6994 (mmm) cc_final: 0.5297 (mtt) REVERT: C 1066 LYS cc_start: 0.7718 (ptmm) cc_final: 0.7493 (ptmm) REVERT: C 1251 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6594 (p-80) REVERT: C 1284 PHE cc_start: 0.7267 (t80) cc_final: 0.6478 (t80) REVERT: C 1287 MET cc_start: 0.6394 (pmm) cc_final: 0.5334 (mmt) REVERT: D 116 TRP cc_start: 0.7327 (OUTLIER) cc_final: 0.6681 (m-10) REVERT: D 131 MET cc_start: 0.8055 (ppp) cc_final: 0.7632 (ppp) REVERT: D 136 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6346 (mm) REVERT: D 239 MET cc_start: 0.6968 (ttt) cc_final: 0.6596 (tpt) REVERT: D 288 ARG cc_start: 0.8446 (ptp-110) cc_final: 0.8183 (mtp85) REVERT: D 310 ASP cc_start: 0.8276 (t0) cc_final: 0.7901 (t0) REVERT: D 421 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5731 (t70) REVERT: D 487 MET cc_start: 0.6821 (mmm) cc_final: 0.6358 (mmm) REVERT: D 550 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (mp) REVERT: D 720 MET cc_start: 0.7448 (mmm) cc_final: 0.7155 (mmm) REVERT: D 730 GLN cc_start: 0.7525 (mt0) cc_final: 0.7056 (tp40) REVERT: D 1143 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6341 (p0) REVERT: D 1150 MET cc_start: 0.6601 (tmm) cc_final: 0.6400 (tmm) REVERT: F 122 MET cc_start: 0.5424 (mmt) cc_final: 0.4165 (mtm) REVERT: F 520 GLU cc_start: 0.7306 (pm20) cc_final: 0.6845 (pm20) REVERT: Q 53 MET cc_start: 0.7043 (mmm) cc_final: 0.6815 (mmm) REVERT: Q 78 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6878 (p) REVERT: Q 211 MET cc_start: 0.3931 (tpt) cc_final: -0.0370 (ptp) REVERT: Q 261 ARG cc_start: 0.7395 (mmp80) cc_final: 0.6947 (ptt-90) REVERT: R 42 MET cc_start: 0.8961 (mmt) cc_final: 0.8580 (mmt) REVERT: R 74 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6483 (m-10) outliers start: 130 outliers final: 87 residues processed: 615 average time/residue: 0.2217 time to fit residues: 218.5281 Evaluate side-chains 625 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 527 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1350 ASN Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 323 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 397 optimal weight: 4.9990 chunk 420 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 391 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1278 GLN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN F 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.250905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176172 restraints weight = 40306.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178650 restraints weight = 24312.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.183759 restraints weight = 14462.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.185860 restraints weight = 9283.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186064 restraints weight = 8224.928| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36541 Z= 0.146 Angle : 0.646 11.539 50022 Z= 0.328 Chirality : 0.042 0.210 5783 Planarity : 0.005 0.079 6142 Dihedral : 16.269 178.879 6081 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.59 % Allowed : 22.58 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4397 helix: 0.37 (0.13), residues: 1663 sheet: -0.66 (0.26), residues: 402 loop : -2.15 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1345 TYR 0.038 0.002 TYR C 201 PHE 0.021 0.001 PHE C 338 TRP 0.021 0.001 TRP D 34 HIS 0.013 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00330 (36535) covalent geometry : angle 0.64279 (50016) hydrogen bonds : bond 0.03929 ( 1390) hydrogen bonds : angle 4.77468 ( 3876) metal coordination : bond 0.01223 ( 6) metal coordination : angle 5.72921 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 539 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.6751 (mmm-85) REVERT: B 4 ARG cc_start: 0.7500 (tpt90) cc_final: 0.7254 (tpt90) REVERT: B 200 LEU cc_start: 0.4248 (OUTLIER) cc_final: 0.3461 (mt) REVERT: C 148 GLU cc_start: 0.7686 (pt0) cc_final: 0.6016 (mt-10) REVERT: C 230 PHE cc_start: 0.8021 (m-80) cc_final: 0.7543 (m-10) REVERT: C 356 ARG cc_start: 0.7384 (tmt170) cc_final: 0.6792 (ttp80) REVERT: C 640 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8406 (mm) REVERT: C 692 MET cc_start: 0.7472 (mtm) cc_final: 0.7197 (mtm) REVERT: C 759 MET cc_start: 0.8095 (mmt) cc_final: 0.7846 (mmt) REVERT: C 817 ASN cc_start: 0.7462 (p0) cc_final: 0.6952 (p0) REVERT: C 901 MET cc_start: 0.7028 (mmm) cc_final: 0.5303 (mtt) REVERT: C 1251 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6633 (p-80) REVERT: C 1287 MET cc_start: 0.6429 (pmm) cc_final: 0.5450 (mmt) REVERT: D 91 VAL cc_start: 0.4941 (OUTLIER) cc_final: 0.4224 (p) REVERT: D 116 TRP cc_start: 0.7325 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: D 239 MET cc_start: 0.6959 (ttt) cc_final: 0.6571 (tpt) REVERT: D 288 ARG cc_start: 0.8322 (ptp-110) cc_final: 0.8043 (mtp85) REVERT: D 310 ASP cc_start: 0.8282 (t0) cc_final: 0.8008 (t0) REVERT: D 404 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7690 (mm-30) REVERT: D 421 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5868 (t70) REVERT: D 487 MET cc_start: 0.6632 (mmm) cc_final: 0.6286 (mtp) REVERT: D 550 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8614 (mp) REVERT: D 711 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7484 (mpt180) REVERT: D 720 MET cc_start: 0.7550 (mmm) cc_final: 0.7299 (mmm) REVERT: D 730 GLN cc_start: 0.7467 (mt0) cc_final: 0.7093 (tp40) REVERT: D 785 LYS cc_start: 0.8883 (mttp) cc_final: 0.8431 (mmtp) REVERT: D 1134 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6483 (tm-30) REVERT: D 1143 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6522 (p0) REVERT: F 122 MET cc_start: 0.5418 (mmt) cc_final: 0.4325 (mtm) REVERT: F 520 GLU cc_start: 0.7289 (pm20) cc_final: 0.6919 (pm20) REVERT: Q 78 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6979 (p) REVERT: Q 211 MET cc_start: 0.3795 (tpt) cc_final: -0.0245 (ptp) REVERT: Q 261 ARG cc_start: 0.7458 (mmp80) cc_final: 0.7038 (ptt-90) REVERT: R 14 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5595 (mmt90) REVERT: R 21 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: R 42 MET cc_start: 0.9032 (mmt) cc_final: 0.8652 (mmt) REVERT: R 74 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6566 (m-10) REVERT: R 218 ASP cc_start: 0.4552 (t0) cc_final: 0.4345 (t0) REVERT: R 287 MET cc_start: 0.5316 (mmm) cc_final: 0.4739 (mmm) outliers start: 154 outliers final: 122 residues processed: 634 average time/residue: 0.2203 time to fit residues: 225.4635 Evaluate side-chains 653 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 519 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1249 LEU Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1200 ILE Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 319 GLU Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 133 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 402 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.245296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171754 restraints weight = 40518.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173096 restraints weight = 24415.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177662 restraints weight = 15297.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179776 restraints weight = 9972.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180287 restraints weight = 8362.601| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36541 Z= 0.216 Angle : 0.739 13.491 50022 Z= 0.378 Chirality : 0.045 0.213 5783 Planarity : 0.005 0.085 6142 Dihedral : 16.410 177.884 6081 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.97 % Allowed : 22.61 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4397 helix: 0.15 (0.13), residues: 1663 sheet: -0.66 (0.27), residues: 393 loop : -2.32 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1345 TYR 0.026 0.002 TYR C 472 PHE 0.022 0.002 PHE R 295 TRP 0.030 0.002 TRP D 34 HIS 0.011 0.002 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00485 (36535) covalent geometry : angle 0.73496 (50016) hydrogen bonds : bond 0.04594 ( 1390) hydrogen bonds : angle 5.10877 ( 3876) metal coordination : bond 0.01584 ( 6) metal coordination : angle 7.18063 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 530 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.6928 (mmm-85) REVERT: A 106 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7706 (mtp-110) REVERT: A 117 GLN cc_start: 0.7454 (mp10) cc_final: 0.7240 (mp10) REVERT: A 125 GLU cc_start: 0.8509 (tp30) cc_final: 0.8219 (tp30) REVERT: B 4 ARG cc_start: 0.7574 (tpt90) cc_final: 0.7004 (tpt90) REVERT: B 96 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6449 (p-80) REVERT: B 200 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.3785 (mt) REVERT: C 201 TYR cc_start: 0.6960 (m-10) cc_final: 0.6713 (m-10) REVERT: C 230 PHE cc_start: 0.8087 (m-80) cc_final: 0.7675 (m-10) REVERT: C 600 ARG cc_start: 0.6331 (tpp80) cc_final: 0.6108 (tpp80) REVERT: C 692 MET cc_start: 0.7630 (mtm) cc_final: 0.7329 (mtm) REVERT: C 701 GLN cc_start: 0.7660 (tt0) cc_final: 0.6965 (tm-30) REVERT: C 732 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7206 (mt-10) REVERT: C 759 MET cc_start: 0.8047 (mmt) cc_final: 0.7777 (mmt) REVERT: C 817 ASN cc_start: 0.7676 (p0) cc_final: 0.7280 (p0) REVERT: C 901 MET cc_start: 0.7142 (mmm) cc_final: 0.5504 (mtt) REVERT: C 1164 GLU cc_start: 0.8112 (pt0) cc_final: 0.7884 (pt0) REVERT: C 1251 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6784 (p-80) REVERT: C 1287 MET cc_start: 0.6928 (pmm) cc_final: 0.6047 (mmt) REVERT: D 91 VAL cc_start: 0.4841 (OUTLIER) cc_final: 0.4087 (p) REVERT: D 116 TRP cc_start: 0.7418 (OUTLIER) cc_final: 0.6863 (m-10) REVERT: D 239 MET cc_start: 0.6948 (ttt) cc_final: 0.6712 (tpt) REVERT: D 288 ARG cc_start: 0.8628 (ptp-110) cc_final: 0.8375 (mtp85) REVERT: D 310 ASP cc_start: 0.8385 (t0) cc_final: 0.8093 (t0) REVERT: D 368 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7321 (p) REVERT: D 404 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7734 (mm-30) REVERT: D 421 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6351 (t70) REVERT: D 443 LEU cc_start: 0.8123 (mm) cc_final: 0.7882 (mp) REVERT: D 487 MET cc_start: 0.6977 (mmm) cc_final: 0.6433 (mmm) REVERT: D 525 GLU cc_start: 0.7207 (tt0) cc_final: 0.6549 (pm20) REVERT: D 550 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8683 (mp) REVERT: D 705 HIS cc_start: 0.7607 (m90) cc_final: 0.7387 (m-70) REVERT: D 720 MET cc_start: 0.7316 (mmm) cc_final: 0.7049 (mmm) REVERT: D 730 GLN cc_start: 0.7492 (mt0) cc_final: 0.7078 (tp40) REVERT: D 1134 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6388 (tm-30) REVERT: D 1143 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6714 (p0) REVERT: F 520 GLU cc_start: 0.7424 (pm20) cc_final: 0.6941 (pm20) REVERT: Q 53 MET cc_start: 0.7077 (mmm) cc_final: 0.6859 (mmm) REVERT: Q 78 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6729 (p) REVERT: Q 211 MET cc_start: 0.4047 (tpt) cc_final: -0.0234 (ptm) REVERT: Q 261 ARG cc_start: 0.7475 (mmp80) cc_final: 0.6960 (ptt-90) REVERT: R 14 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.5639 (mmt90) REVERT: R 42 MET cc_start: 0.9040 (mmt) cc_final: 0.8672 (mmt) REVERT: R 74 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6702 (m-10) outliers start: 200 outliers final: 149 residues processed: 662 average time/residue: 0.2140 time to fit residues: 230.2726 Evaluate side-chains 682 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 521 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1249 LEU Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1146 VAL Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1200 ILE Chi-restraints excluded: chain D residue 1204 GLU Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 482 ILE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 319 GLU Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 375 optimal weight: 8.9990 chunk 368 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 365 optimal weight: 2.9990 chunk 418 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C1126 ASN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 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 = 0.4893 r_free = 0.4893 target = 0.250065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.175287 restraints weight = 40348.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178237 restraints weight = 24604.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.182768 restraints weight = 14453.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.185212 restraints weight = 9575.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185484 restraints weight = 7811.189| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36541 Z= 0.145 Angle : 0.665 12.416 50022 Z= 0.336 Chirality : 0.043 0.395 5783 Planarity : 0.005 0.069 6142 Dihedral : 16.316 177.148 6081 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.92 % Allowed : 24.19 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.13), residues: 4397 helix: 0.34 (0.13), residues: 1675 sheet: -0.66 (0.26), residues: 403 loop : -2.19 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1345 TYR 0.016 0.002 TYR A 176 PHE 0.018 0.001 PHE R 295 TRP 0.019 0.001 TRP D 34 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00330 (36535) covalent geometry : angle 0.66297 (50016) hydrogen bonds : bond 0.03912 ( 1390) hydrogen bonds : angle 4.75995 ( 3876) metal coordination : bond 0.01242 ( 6) metal coordination : angle 5.29790 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 544 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.6834 (mmm-85) REVERT: A 106 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7796 (mtp-110) REVERT: A 117 GLN cc_start: 0.7511 (mp10) cc_final: 0.7240 (mp10) REVERT: B 4 ARG cc_start: 0.7448 (tpt90) cc_final: 0.7204 (tpt90) REVERT: B 96 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6357 (p-80) REVERT: B 102 ARG cc_start: 0.8683 (tpp80) cc_final: 0.8005 (tpp80) REVERT: B 103 MET cc_start: 0.6861 (tpt) cc_final: 0.6412 (tpt) REVERT: B 125 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 200 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3439 (mt) REVERT: C 148 GLU cc_start: 0.7716 (pt0) cc_final: 0.5977 (mt-10) REVERT: C 230 PHE cc_start: 0.8010 (m-80) cc_final: 0.7538 (m-10) REVERT: C 336 GLN cc_start: 0.4854 (OUTLIER) cc_final: 0.4626 (pp30) REVERT: C 356 ARG cc_start: 0.7186 (tmt170) cc_final: 0.6799 (ttp-170) REVERT: C 759 MET cc_start: 0.8168 (mmt) cc_final: 0.7885 (mmt) REVERT: C 817 ASN cc_start: 0.7429 (p0) cc_final: 0.6948 (p0) REVERT: C 901 MET cc_start: 0.7230 (mmm) cc_final: 0.5604 (mtt) REVERT: C 1164 GLU cc_start: 0.8061 (pt0) cc_final: 0.7812 (pt0) REVERT: C 1165 ARG cc_start: 0.8010 (ptt90) cc_final: 0.7714 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6717 (p-80) REVERT: C 1287 MET cc_start: 0.6643 (pmm) cc_final: 0.5877 (mmt) REVERT: D 91 VAL cc_start: 0.4841 (OUTLIER) cc_final: 0.4073 (p) REVERT: D 116 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.6889 (m-10) REVERT: D 239 MET cc_start: 0.6937 (ttt) cc_final: 0.6711 (tpt) REVERT: D 288 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8161 (mtp85) REVERT: D 310 ASP cc_start: 0.8276 (t0) cc_final: 0.7962 (t0) REVERT: D 404 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 421 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6122 (t70) REVERT: D 487 MET cc_start: 0.6732 (mmm) cc_final: 0.6210 (mmm) REVERT: D 490 ASN cc_start: 0.8134 (m-40) cc_final: 0.7889 (m-40) REVERT: D 525 GLU cc_start: 0.7084 (tt0) cc_final: 0.6511 (pm20) REVERT: D 550 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8614 (mp) REVERT: D 711 ARG cc_start: 0.7784 (mpt180) cc_final: 0.7551 (mpt180) REVERT: D 720 MET cc_start: 0.7685 (mmm) cc_final: 0.7439 (mmm) REVERT: D 730 GLN cc_start: 0.7418 (mt0) cc_final: 0.7044 (tp40) REVERT: D 1134 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6434 (tm-30) REVERT: D 1143 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6310 (p0) REVERT: D 1235 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7496 (tm-30) REVERT: F 520 GLU cc_start: 0.7387 (pm20) cc_final: 0.6915 (pm20) REVERT: Q 53 MET cc_start: 0.6806 (mmm) cc_final: 0.6571 (mmm) REVERT: Q 78 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6864 (p) REVERT: Q 211 MET cc_start: 0.3656 (tpt) cc_final: -0.0274 (ptm) REVERT: Q 261 ARG cc_start: 0.7525 (mmp80) cc_final: 0.7063 (ptt-90) REVERT: R 14 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5490 (mmt90) REVERT: R 15 MET cc_start: 0.4918 (ptm) cc_final: 0.4654 (ptp) REVERT: R 42 MET cc_start: 0.9020 (mmt) cc_final: 0.8650 (mmt) REVERT: R 74 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6893 (m-10) outliers start: 165 outliers final: 128 residues processed: 652 average time/residue: 0.2203 time to fit residues: 230.2634 Evaluate side-chains 674 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 534 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 803 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1146 VAL Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 319 GLU Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 195 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 190 optimal weight: 0.2980 chunk 219 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 422 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.248410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172389 restraints weight = 40556.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175033 restraints weight = 24924.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.179442 restraints weight = 15138.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181544 restraints weight = 10089.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181725 restraints weight = 8232.439| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36541 Z= 0.168 Angle : 0.699 13.728 50022 Z= 0.353 Chirality : 0.044 0.430 5783 Planarity : 0.005 0.091 6142 Dihedral : 16.366 175.562 6081 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.04 % Allowed : 24.79 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.53 (0.13), residues: 4397 helix: 0.37 (0.13), residues: 1661 sheet: -0.61 (0.27), residues: 399 loop : -2.22 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1345 TYR 0.019 0.002 TYR C 472 PHE 0.020 0.001 PHE C 338 TRP 0.022 0.001 TRP D 34 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00381 (36535) covalent geometry : angle 0.69619 (50016) hydrogen bonds : bond 0.04084 ( 1390) hydrogen bonds : angle 4.79919 ( 3876) metal coordination : bond 0.01270 ( 6) metal coordination : angle 5.44658 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 529 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6895 (mmm-85) REVERT: A 106 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7871 (mtp-110) REVERT: A 117 GLN cc_start: 0.7450 (mp10) cc_final: 0.7116 (mp10) REVERT: A 125 GLU cc_start: 0.8381 (tp30) cc_final: 0.8156 (tp30) REVERT: B 4 ARG cc_start: 0.7546 (tpt90) cc_final: 0.7278 (tpt90) REVERT: B 96 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6307 (p-80) REVERT: B 102 ARG cc_start: 0.8593 (tpp80) cc_final: 0.7908 (tpp80) REVERT: B 103 MET cc_start: 0.6865 (tpt) cc_final: 0.6476 (tpt) REVERT: B 200 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3715 (mt) REVERT: C 230 PHE cc_start: 0.7985 (m-80) cc_final: 0.7562 (m-10) REVERT: C 356 ARG cc_start: 0.7147 (tmt170) cc_final: 0.6770 (ttp-170) REVERT: C 759 MET cc_start: 0.8128 (mmt) cc_final: 0.7861 (mmt) REVERT: C 817 ASN cc_start: 0.7535 (p0) cc_final: 0.7153 (p0) REVERT: C 847 ARG cc_start: 0.4784 (OUTLIER) cc_final: 0.3892 (mtp-110) REVERT: C 901 MET cc_start: 0.7246 (mmm) cc_final: 0.5664 (mtt) REVERT: C 1164 GLU cc_start: 0.8086 (pt0) cc_final: 0.7842 (pt0) REVERT: C 1165 ARG cc_start: 0.7994 (ptt90) cc_final: 0.7678 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6655 (p-80) REVERT: C 1287 MET cc_start: 0.6845 (pmm) cc_final: 0.6157 (mmt) REVERT: D 91 VAL cc_start: 0.4843 (OUTLIER) cc_final: 0.4129 (p) REVERT: D 116 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6795 (m-10) REVERT: D 239 MET cc_start: 0.7089 (ttt) cc_final: 0.6858 (tpt) REVERT: D 288 ARG cc_start: 0.8411 (ptp-110) cc_final: 0.8142 (mtp85) REVERT: D 310 ASP cc_start: 0.8320 (t0) cc_final: 0.8000 (t0) REVERT: D 404 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7698 (mm-30) REVERT: D 421 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6263 (t70) REVERT: D 487 MET cc_start: 0.6777 (mmm) cc_final: 0.6201 (mmm) REVERT: D 490 ASN cc_start: 0.8130 (m-40) cc_final: 0.7882 (m-40) REVERT: D 525 GLU cc_start: 0.7300 (tt0) cc_final: 0.6617 (pm20) REVERT: D 550 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8610 (mp) REVERT: D 730 GLN cc_start: 0.7491 (mt0) cc_final: 0.7083 (tp40) REVERT: D 1134 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6399 (tm-30) REVERT: D 1143 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6245 (p0) REVERT: D 1150 MET cc_start: 0.7089 (tpp) cc_final: 0.6459 (tpp) REVERT: D 1328 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7310 (tt) REVERT: F 520 GLU cc_start: 0.7508 (pm20) cc_final: 0.7046 (pm20) REVERT: Q 78 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6811 (p) REVERT: Q 211 MET cc_start: 0.3975 (tpt) cc_final: -0.0030 (ptm) REVERT: Q 261 ARG cc_start: 0.7441 (mmp80) cc_final: 0.6989 (ptt-90) REVERT: R 14 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5486 (mmt90) REVERT: R 42 MET cc_start: 0.9055 (mmt) cc_final: 0.8679 (mmt) REVERT: R 74 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6926 (m-10) outliers start: 169 outliers final: 142 residues processed: 641 average time/residue: 0.2115 time to fit residues: 220.2093 Evaluate side-chains 682 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 527 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1082 ASP Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1196 ILE Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1249 LEU Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1268 VAL Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 803 CYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1146 VAL Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1200 ILE Chi-restraints excluded: chain D residue 1237 TYR Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 LEU Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 482 ILE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 319 GLU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 324 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 217 optimal weight: 0.5980 chunk 314 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 440 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 246 optimal weight: 0.0980 chunk 335 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 ASN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.256014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.180384 restraints weight = 40567.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182558 restraints weight = 23908.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.186546 restraints weight = 14726.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189364 restraints weight = 9872.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.190099 restraints weight = 7853.512| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36541 Z= 0.118 Angle : 0.656 14.128 50022 Z= 0.326 Chirality : 0.042 0.375 5783 Planarity : 0.005 0.096 6142 Dihedral : 16.274 174.883 6081 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.01 % Allowed : 26.82 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4397 helix: 0.59 (0.13), residues: 1664 sheet: -0.51 (0.26), residues: 401 loop : -2.09 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1345 TYR 0.042 0.001 TYR C 201 PHE 0.027 0.001 PHE C 393 TRP 0.017 0.001 TRP C 813 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00265 (36535) covalent geometry : angle 0.65453 (50016) hydrogen bonds : bond 0.03489 ( 1390) hydrogen bonds : angle 4.44033 ( 3876) metal coordination : bond 0.00933 ( 6) metal coordination : angle 3.50958 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8794 Ramachandran restraints generated. 4397 Oldfield, 0 Emsley, 4397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 539 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6771 (mmm-85) REVERT: A 106 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7545 (mtp-110) REVERT: A 117 GLN cc_start: 0.7404 (mp10) cc_final: 0.7078 (mp10) REVERT: A 125 GLU cc_start: 0.8374 (tp30) cc_final: 0.8164 (tp30) REVERT: B 102 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7813 (tpp80) REVERT: B 103 MET cc_start: 0.6578 (tpt) cc_final: 0.6279 (tpt) REVERT: B 125 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 200 LEU cc_start: 0.4120 (OUTLIER) cc_final: 0.3468 (mt) REVERT: C 148 GLU cc_start: 0.7217 (pt0) cc_final: 0.5548 (mt-10) REVERT: C 294 LEU cc_start: -0.2830 (OUTLIER) cc_final: -0.3109 (pp) REVERT: C 600 ARG cc_start: 0.6367 (tpp80) cc_final: 0.6145 (tpp80) REVERT: C 817 ASN cc_start: 0.7132 (p0) cc_final: 0.6735 (p0) REVERT: C 901 MET cc_start: 0.7215 (mmm) cc_final: 0.5583 (mtt) REVERT: C 1083 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7850 (ttmt) REVERT: C 1124 ARG cc_start: 0.6710 (ptp-170) cc_final: 0.6435 (ptp-170) REVERT: C 1164 GLU cc_start: 0.8021 (pt0) cc_final: 0.7791 (pt0) REVERT: C 1165 ARG cc_start: 0.7850 (ptt90) cc_final: 0.7407 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6507 (p-80) REVERT: C 1287 MET cc_start: 0.6020 (pmm) cc_final: 0.5311 (mmt) REVERT: C 1330 GLU cc_start: 0.6680 (mm-30) cc_final: 0.5853 (mt-10) REVERT: D 91 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4484 (p) REVERT: D 116 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: D 239 MET cc_start: 0.6913 (ttt) cc_final: 0.6687 (tpt) REVERT: D 288 ARG cc_start: 0.8182 (ptp-110) cc_final: 0.7869 (mtp85) REVERT: D 310 ASP cc_start: 0.8122 (t0) cc_final: 0.7829 (t0) REVERT: D 404 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7640 (mm-30) REVERT: D 490 ASN cc_start: 0.7971 (m-40) cc_final: 0.7729 (m-40) REVERT: D 539 MET cc_start: 0.6918 (tpt) cc_final: 0.6700 (tpt) REVERT: D 566 LYS cc_start: 0.8245 (tttt) cc_final: 0.7523 (tptm) REVERT: D 720 MET cc_start: 0.7339 (mmm) cc_final: 0.7101 (mmm) REVERT: D 730 GLN cc_start: 0.7324 (mt0) cc_final: 0.7028 (tp40) REVERT: D 879 ARG cc_start: 0.5946 (ttt90) cc_final: 0.5675 (tpt170) REVERT: D 1143 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6103 (p0) REVERT: D 1150 MET cc_start: 0.6742 (tpp) cc_final: 0.6075 (tpp) REVERT: D 1155 GLU cc_start: 0.8027 (pt0) cc_final: 0.7475 (pp20) REVERT: D 1235 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7382 (tm-30) REVERT: D 1323 GLU cc_start: 0.6804 (tp30) cc_final: 0.6341 (tp30) REVERT: F 520 GLU cc_start: 0.7273 (pm20) cc_final: 0.6955 (pm20) REVERT: Q 211 MET cc_start: 0.3558 (tpt) cc_final: -0.0132 (ptp) REVERT: Q 261 ARG cc_start: 0.7501 (mmp80) cc_final: 0.7067 (ptt-90) REVERT: R 14 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5452 (mmt90) REVERT: R 23 LEU cc_start: 0.7162 (pp) cc_final: 0.6889 (mt) REVERT: R 42 MET cc_start: 0.8993 (mmt) cc_final: 0.8625 (mmt) REVERT: R 74 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6952 (m-10) outliers start: 101 outliers final: 79 residues processed: 612 average time/residue: 0.2183 time to fit residues: 215.4425 Evaluate side-chains 607 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 520 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 1082 ASP Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1223 GLN Chi-restraints excluded: chain C residue 1251 HIS Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1318 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1200 ILE Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1305 ILE Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1349 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 287 MET Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 313 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 28 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 363 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 408 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 763 GLN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.255657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.180032 restraints weight = 40475.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.182316 restraints weight = 24199.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.186632 restraints weight = 14072.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188482 restraints weight = 9669.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.189311 restraints weight = 8302.053| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 36541 Z= 0.171 Angle : 0.747 59.080 50022 Z= 0.397 Chirality : 0.044 0.846 5783 Planarity : 0.005 0.104 6142 Dihedral : 16.277 174.881 6081 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.92 % Allowed : 27.09 % Favored : 69.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4397 helix: 0.58 (0.13), residues: 1665 sheet: -0.50 (0.26), residues: 401 loop : -2.09 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG Q 36 TYR 0.032 0.001 TYR C 201 PHE 0.025 0.001 PHE C 393 TRP 0.016 0.001 TRP D 116 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00363 (36535) covalent geometry : angle 0.74597 (50016) hydrogen bonds : bond 0.03498 ( 1390) hydrogen bonds : angle 4.44620 ( 3876) metal coordination : bond 0.00961 ( 6) metal coordination : angle 3.51330 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7449.42 seconds wall clock time: 128 minutes 16.09 seconds (7696.09 seconds total)