Starting phenix.real_space_refine on Sun Aug 9 17:36:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pga_71624/08_2026/9pga_71624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pga_71624/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9pga_71624/08_2026/9pga_71624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pga_71624/08_2026/9pga_71624.map" model { file = "/net/cci-nas-00/data/ceres_data/9pga_71624/08_2026/9pga_71624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pga_71624/08_2026/9pga_71624.cif" } 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-2.2rc3-6140/lib/python3.11/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: 6.55, per 1000 atoms: 0.18 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: 2.78 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: 4.24 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: 8.67 Time building geometry restraints manager: 3.56 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=" C1' DC H 0 " pdb=" N1 DC H 0 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C3' DT H 7 " pdb=" C2' DT H 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C1' DT I 41 " pdb=" N1 DT I 41 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.49e+00 bond pdb=" C3' DC H 17 " pdb=" C2' DC H 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.87e+00 bond pdb=" C1' DT H -2 " pdb=" N1 DT H -2 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.49e+00 ... (remaining 36530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 49097 2.23 - 4.45: 809 4.45 - 6.68: 90 6.68 - 8.90: 16 8.90 - 11.13: 4 Bond angle restraints: 50016 Sorted by residual: angle pdb=" O4' DG H 5 " pdb=" C4' DG H 5 " pdb=" C3' DG H 5 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.33e+01 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=" O4' DG I 34 " pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+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=" N3 DT I -13 " pdb=" C4 DT I -13 " pdb=" O4 DT I -13 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+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: 3783 0.038 - 0.075: 1410 0.075 - 0.113: 490 0.113 - 0.150: 94 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 2.34 -2.51 -0.17 2.00e-01 2.50e+01 7.62e-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: 5.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 37.280 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 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= 0.251 Angle : 0.703 11.130 50022 Z= 0.418 Chirality : 0.044 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/Z covalent geometry : bond 0.00426 / 0.25 (36535) covalent geometry : angle 0.70140 / 0.42 (50016) hydrogen bonds : bond 0.16293 / 11.08 ( 1390) hydrogen bonds : angle 6.52316 / 4.55 ( 3876) metal coordination : bond 0.01286 / 0.60 ( 6) metal coordination : angle 4.66715 / 2.40 ( 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 : 0.960 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: 0.2293 time to fit residues: 214.9176 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 : 0.909 ------------------------------------------------------------------------------- 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... A 128 ASN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 268 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 GLN Q 245 GLN ** 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 = 0.4952 r_free = 0.4952 target = 0.257363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.178294 restraints weight = 40758.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.182294 restraints weight = 25193.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186578 restraints weight = 15107.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.189631 restraints weight = 10303.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.190621 restraints weight = 8136.427| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.0889 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= 0.164 Angle : 0.672 11.505 50022 Z= 0.348 Chirality : 0.044 0.224 5783 Planarity : 0.005 0.080 6142 Dihedral : 16.188 177.520 6081 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.67 % Allowed : 10.89 % Favored : 87.44 % 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: -1.56 (0.12), residues: 4397 helix: 0.23 (0.13), residues: 1661 sheet: -0.74 (0.25), residues: 429 loop : -2.12 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 271 TYR 0.027 0.002 TYR C 472 PHE 0.022 0.001 PHE C 513 TRP 0.028 0.001 TRP D 34 HIS 0.006 0.001 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (36535) covalent geometry : angle 0.67013 / 0.35 (50016) hydrogen bonds : bond 0.04877 / 3.28 ( 1390) hydrogen bonds : angle 5.29007 / 3.68 ( 3876) metal coordination : bond 0.01117 / 0.53 ( 6) metal coordination : angle 4.07352 / 2.16 ( 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: 56 poor density : 553 time to evaluate : 1.193 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: B 4 ARG cc_start: 0.7481 (tpt90) cc_final: 0.7097 (tpt90) REVERT: B 80 ASP cc_start: 0.8784 (t0) cc_final: 0.8513 (t0) REVERT: B 125 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 438 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8117 (mmtp) REVERT: C 532 ILE cc_start: 0.8339 (tp) cc_final: 0.8073 (tp) REVERT: C 692 MET cc_start: 0.7629 (mtm) cc_final: 0.7168 (mtm) REVERT: C 901 MET cc_start: 0.6046 (mmm) cc_final: 0.4495 (mtt) REVERT: C 920 ARG cc_start: 0.6897 (ptt180) cc_final: 0.6246 (tmm-80) REVERT: C 1260 ARG cc_start: 0.8055 (ttt-90) cc_final: 0.7248 (ttt-90) REVERT: C 1287 MET cc_start: 0.6312 (pmm) cc_final: 0.5331 (mmt) REVERT: D 539 MET cc_start: 0.7261 (tpt) cc_final: 0.7060 (tpt) REVERT: D 614 GLN cc_start: 0.7762 (pp30) cc_final: 0.7443 (pp30) REVERT: D 711 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7510 (mpt180) REVERT: D 730 GLN cc_start: 0.7819 (mt0) cc_final: 0.7158 (tp40) REVERT: D 740 ARG cc_start: 0.3545 (mtp180) cc_final: 0.2858 (mtp180) REVERT: D 1143 ASP cc_start: 0.6566 (p0) cc_final: 0.6207 (p0) REVERT: D 1150 MET cc_start: 0.7048 (tmm) cc_final: 0.6484 (tmm) REVERT: E 7 GLU cc_start: 0.7921 (mp0) cc_final: 0.7656 (mp0) REVERT: Q 86 ARG cc_start: 0.7727 (tpm170) cc_final: 0.7493 (tpm170) REVERT: R 42 MET cc_start: 0.8875 (mmt) cc_final: 0.8481 (mmt) outliers start: 56 outliers final: 42 residues processed: 577 average time/residue: 0.2349 time to fit residues: 215.8018 Evaluate side-chains 566 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 524 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 119 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 105 LEU 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 198 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 336 GLN 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 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 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 Chi-restraints excluded: chain R residue 313 MET 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: 0.7980 chunk 437 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 169 optimal weight: 0.0020 chunk 120 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 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 ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1278 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS ** R 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.257066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.179801 restraints weight = 39767.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.184881 restraints weight = 22808.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.190023 restraints weight = 14442.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.193034 restraints weight = 9258.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.193555 restraints weight = 7457.099| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36541 Z= 0.132 Angle : 0.624 10.049 50022 Z= 0.321 Chirality : 0.043 0.235 5783 Planarity : 0.005 0.060 6142 Dihedral : 16.161 176.903 6081 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.97 % Allowed : 15.51 % Favored : 82.52 % 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: -1.41 (0.13), residues: 4397 helix: 0.39 (0.13), residues: 1659 sheet: -0.57 (0.25), residues: 414 loop : -2.08 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1345 TYR 0.024 0.001 TYR C 201 PHE 0.027 0.001 PHE C 338 TRP 0.023 0.001 TRP D 34 HIS 0.005 0.001 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (36535) covalent geometry : angle 0.62071 / 0.32 (50016) hydrogen bonds : bond 0.04317 / 2.91 ( 1390) hydrogen bonds : angle 4.94472 / 3.43 ( 3876) metal coordination : bond 0.01107 / 0.51 ( 6) metal coordination : angle 5.59121 / 2.89 ( 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 617 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 551 time to evaluate : 1.073 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: symmetry clash REVERT: A 28 ARG cc_start: 0.7341 (mmm-85) cc_final: 0.6975 (mmm-85) REVERT: B 4 ARG cc_start: 0.7423 (tpt90) cc_final: 0.7005 (tpt90) REVERT: B 80 ASP cc_start: 0.8854 (t0) cc_final: 0.8486 (t0) REVERT: C 532 ILE cc_start: 0.8464 (tp) cc_final: 0.8142 (tp) REVERT: C 614 MET cc_start: 0.7392 (mmt) cc_final: 0.7090 (mmp) REVERT: C 692 MET cc_start: 0.7580 (mtm) cc_final: 0.7151 (mtm) REVERT: C 901 MET cc_start: 0.6086 (mmm) cc_final: 0.4516 (mtt) REVERT: C 920 ARG cc_start: 0.6834 (ptt180) cc_final: 0.6218 (tmm-80) REVERT: C 1287 MET cc_start: 0.6177 (pmm) cc_final: 0.5162 (mmt) REVERT: D 239 MET cc_start: 0.6840 (ttt) cc_final: 0.6401 (tpt) REVERT: D 310 ASP cc_start: 0.8170 (t0) cc_final: 0.7849 (t0) REVERT: D 720 MET cc_start: 0.7355 (mmm) cc_final: 0.7036 (mmm) REVERT: D 730 GLN cc_start: 0.7657 (mt0) cc_final: 0.7113 (tp40) REVERT: D 1143 ASP cc_start: 0.6659 (p0) cc_final: 0.6160 (p0) REVERT: D 1150 MET cc_start: 0.6746 (tmm) cc_final: 0.6004 (tmm) REVERT: D 1155 GLU cc_start: 0.7894 (pt0) cc_final: 0.7660 (pp20) REVERT: Q 86 ARG cc_start: 0.7795 (tpm170) cc_final: 0.7556 (tpm170) REVERT: R 42 MET cc_start: 0.8870 (mmt) cc_final: 0.8459 (mmt) outliers start: 66 outliers final: 45 residues processed: 577 average time/residue: 0.2083 time to fit residues: 191.9149 Evaluate side-chains 562 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 517 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain B residue 84 ILE 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 B residue 223 LEU 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 612 VAL 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 1223 GLN Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain D residue 47 TYR 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 368 CYS 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 898 ASP Chi-restraints excluded: chain D residue 903 THR Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 123 VAL 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: 0.8980 chunk 246 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 365 optimal weight: 1.9990 chunk 403 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 374 optimal weight: 0.9980 chunk 282 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 chunk 446 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 295 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN 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 C1302 GLN ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 479 GLN D1285 GLN D1334 HIS Q 225 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.251135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.177362 restraints weight = 40207.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180172 restraints weight = 23241.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.184441 restraints weight = 13620.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186548 restraints weight = 9190.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.187019 restraints weight = 7737.523| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36541 Z= 0.196 Angle : 0.678 11.344 50022 Z= 0.352 Chirality : 0.044 0.241 5783 Planarity : 0.005 0.062 6142 Dihedral : 16.213 176.836 6081 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.61 % Allowed : 17.96 % Favored : 78.43 % 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: -1.56 (0.12), residues: 4397 helix: 0.26 (0.13), residues: 1667 sheet: -0.54 (0.26), residues: 406 loop : -2.20 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 100 TYR 0.030 0.002 TYR C 472 PHE 0.024 0.002 PHE R 295 TRP 0.025 0.002 TRP D 34 HIS 0.010 0.001 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (36535) covalent geometry : angle 0.67443 / 0.35 (50016) hydrogen bonds : bond 0.04447 / 3.02 ( 1390) hydrogen bonds : angle 5.02561 / 3.49 ( 3876) metal coordination : bond 0.01497 / 0.63 ( 6) metal coordination : angle 6.52238 / 3.46 ( 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 655 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 534 time to evaluate : 0.932 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: 0.7447 (mmm-85) cc_final: 0.6976 (mmm-85) REVERT: B 4 ARG cc_start: 0.7532 (tpt90) cc_final: 0.7015 (tpt90) REVERT: B 51 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6658 (mp) REVERT: B 80 ASP cc_start: 0.8816 (t0) cc_final: 0.8448 (t0) REVERT: C 660 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.5022 (ppp) REVERT: C 692 MET cc_start: 0.7587 (mtm) cc_final: 0.7124 (mtm) REVERT: C 901 MET cc_start: 0.6318 (mmm) cc_final: 0.4671 (mtt) REVERT: C 920 ARG cc_start: 0.6955 (ptt180) cc_final: 0.6672 (ttp-170) REVERT: C 926 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5611 (tt) REVERT: C 1251 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6560 (p-80) REVERT: C 1260 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7134 (ttt-90) REVERT: C 1287 MET cc_start: 0.6383 (pmm) cc_final: 0.5538 (mmt) REVERT: C 1304 MET cc_start: 0.6632 (tpp) cc_final: 0.6343 (tpp) REVERT: C 1351 VAL cc_start: 0.4765 (OUTLIER) cc_final: 0.4516 (p) REVERT: D 116 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: D 125 ILE cc_start: 0.4762 (OUTLIER) cc_final: 0.4310 (tp) REVERT: D 238 TRP cc_start: 0.7488 (m-90) cc_final: 0.6611 (m-90) REVERT: D 239 MET cc_start: 0.6823 (ttt) cc_final: 0.6412 (tpt) REVERT: D 288 ARG cc_start: 0.8375 (ptp-110) cc_final: 0.8089 (mtp85) REVERT: D 550 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8673 (mp) REVERT: D 614 GLN cc_start: 0.7764 (pp30) cc_final: 0.7419 (pp30) REVERT: D 720 MET cc_start: 0.7169 (mmm) cc_final: 0.6771 (mmm) REVERT: D 730 GLN cc_start: 0.7725 (mt0) cc_final: 0.7159 (tp40) REVERT: D 1143 ASP cc_start: 0.6817 (p0) cc_final: 0.6258 (p0) REVERT: D 1150 MET cc_start: 0.6887 (tmm) cc_final: 0.5851 (tmm) REVERT: D 1256 MET cc_start: 0.7303 (tmm) cc_final: 0.7098 (tmm) REVERT: F 520 GLU cc_start: 0.7256 (pm20) cc_final: 0.6865 (pm20) REVERT: R 42 MET cc_start: 0.8892 (mmt) cc_final: 0.8580 (mmm) REVERT: R 218 ASP cc_start: 0.4566 (t0) cc_final: 0.4362 (t0) outliers start: 121 outliers final: 87 residues processed: 599 average time/residue: 0.2057 time to fit residues: 198.8755 Evaluate side-chains 597 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 502 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 214 ASP 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 105 LEU 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 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 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 612 VAL 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 756 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 926 LEU 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 1307 VAL Chi-restraints excluded: chain C residue 1323 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1351 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 136 ILE 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 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 383 ILE Chi-restraints excluded: chain D residue 410 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 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 654 VAL 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 928 MET Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 1186 ILE 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 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 471 THR 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 646 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 309 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: 2.9990 chunk 58 optimal weight: 1.9990 chunk 413 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 404 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN ** 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 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** 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 158 HIS ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.250627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179996 restraints weight = 40319.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.180658 restraints weight = 24102.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185464 restraints weight = 14691.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186510 restraints weight = 9690.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.187381 restraints weight = 8470.039| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36541 Z= 0.184 Angle : 0.677 12.744 50022 Z= 0.347 Chirality : 0.044 0.298 5783 Planarity : 0.005 0.076 6142 Dihedral : 16.229 176.688 6081 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.30 % Allowed : 20.11 % Favored : 75.60 % 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: -1.61 (0.12), residues: 4397 helix: 0.23 (0.13), residues: 1665 sheet: -0.59 (0.26), residues: 406 loop : -2.22 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 100 TYR 0.024 0.002 TYR C 472 PHE 0.031 0.002 PHE R 295 TRP 0.024 0.001 TRP D 34 HIS 0.007 0.001 HIS C1251 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (36535) covalent geometry : angle 0.66963 / 0.35 (50016) hydrogen bonds : bond 0.04347 / 2.96 ( 1390) hydrogen bonds : angle 5.00378 / 3.46 ( 3876) metal coordination : bond 0.01702 / 0.68 ( 6) metal coordination : angle 9.08173 / 4.78 ( 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 666 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 522 time to evaluate : 1.113 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: 0.7476 (mmm-85) cc_final: 0.6977 (mmm-85) REVERT: B 4 ARG cc_start: 0.7521 (tpt90) cc_final: 0.6983 (tpt90) REVERT: B 80 ASP cc_start: 0.8820 (t0) cc_final: 0.8423 (t0) REVERT: C 230 PHE cc_start: 0.8097 (m-80) cc_final: 0.7625 (m-10) REVERT: C 614 MET cc_start: 0.7443 (mmt) cc_final: 0.7152 (mmp) REVERT: C 660 MET cc_start: 0.5263 (OUTLIER) cc_final: 0.4979 (ppp) REVERT: C 692 MET cc_start: 0.7544 (mtm) cc_final: 0.7083 (mtm) REVERT: C 901 MET cc_start: 0.6519 (mmm) cc_final: 0.5037 (mtt) REVERT: C 920 ARG cc_start: 0.6991 (ptt180) cc_final: 0.6674 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6549 (p-80) REVERT: C 1260 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7030 (ttt-90) REVERT: C 1287 MET cc_start: 0.6367 (pmm) cc_final: 0.5550 (mmt) REVERT: C 1304 MET cc_start: 0.6699 (tpp) cc_final: 0.6409 (tpp) REVERT: D 116 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6716 (m-10) REVERT: D 131 MET cc_start: 0.8148 (ppp) cc_final: 0.7947 (ppp) REVERT: D 238 TRP cc_start: 0.7474 (m-90) cc_final: 0.6607 (m-90) REVERT: D 239 MET cc_start: 0.6939 (ttt) cc_final: 0.6583 (tpt) REVERT: D 288 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.8204 (mtp85) REVERT: D 421 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.4477 (t70) REVERT: D 550 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (mp) REVERT: D 720 MET cc_start: 0.7355 (mmm) cc_final: 0.7063 (mmm) REVERT: D 730 GLN cc_start: 0.7637 (mt0) cc_final: 0.7119 (tp40) REVERT: D 1143 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6322 (p0) REVERT: D 1150 MET cc_start: 0.6760 (tmm) cc_final: 0.5921 (tmm) REVERT: F 520 GLU cc_start: 0.7264 (pm20) cc_final: 0.6831 (pm20) REVERT: F 526 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (mm) REVERT: Q 211 MET cc_start: 0.3578 (tpt) cc_final: -0.0733 (ptp) REVERT: R 42 MET cc_start: 0.8870 (mmt) cc_final: 0.8519 (mmm) REVERT: R 74 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6239 (m-10) REVERT: R 287 MET cc_start: 0.4839 (mmm) cc_final: 0.4609 (mmm) outliers start: 144 outliers final: 103 residues processed: 611 average time/residue: 0.1994 time to fit residues: 197.2743 Evaluate side-chains 620 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 509 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 119 GLU 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 214 ASP Chi-restraints excluded: chain B residue 84 ILE 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 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 216 LEU 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 371 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 450 ILE 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 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 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 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 116 TRP Chi-restraints excluded: chain D residue 136 ILE 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 383 ILE Chi-restraints excluded: chain D residue 392 LEU 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 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 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 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 1301 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 471 THR 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 526 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 548 THR 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 270 VAL 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 82 LEU 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: 0.0970 chunk 302 optimal weight: 8.9990 chunk 312 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 397 optimal weight: 0.6980 chunk 420 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 391 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 626 GLN C1126 ASN C1278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.254721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.181723 restraints weight = 39996.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.183451 restraints weight = 24113.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.187231 restraints weight = 15132.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.189679 restraints weight = 9988.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.190050 restraints weight = 8038.905| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36541 Z= 0.128 Angle : 0.633 11.431 50022 Z= 0.323 Chirality : 0.043 0.249 5783 Planarity : 0.005 0.150 6142 Dihedral : 16.175 176.954 6081 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.64 % Allowed : 21.48 % Favored : 74.88 % 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: -1.37 (0.13), residues: 4397 helix: 0.46 (0.13), residues: 1661 sheet: -0.49 (0.26), residues: 400 loop : -2.10 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1345 TYR 0.024 0.001 TYR C 201 PHE 0.038 0.001 PHE R 295 TRP 0.020 0.001 TRP D 34 HIS 0.005 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (36535) covalent geometry : angle 0.62997 / 0.32 (50016) hydrogen bonds : bond 0.03900 / 2.66 ( 1390) hydrogen bonds : angle 4.73537 / 3.27 ( 3876) metal coordination : bond 0.01074 / 0.45 ( 6) metal coordination : angle 5.21798 / 2.78 ( 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 658 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 536 time to evaluate : 1.851 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: 0.7466 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: A 119 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.5240 (tp30) REVERT: B 4 ARG cc_start: 0.7369 (tpt90) cc_final: 0.7128 (tpt90) REVERT: B 51 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6608 (mp) REVERT: C 230 PHE cc_start: 0.8055 (m-80) cc_final: 0.7594 (m-10) REVERT: C 356 ARG cc_start: 0.7321 (tmt170) cc_final: 0.6839 (tmm160) REVERT: C 532 ILE cc_start: 0.8550 (tp) cc_final: 0.8149 (tp) REVERT: C 660 MET cc_start: 0.5215 (OUTLIER) cc_final: 0.4906 (ppp) REVERT: C 692 MET cc_start: 0.7504 (mtm) cc_final: 0.7163 (mtm) REVERT: C 817 ASN cc_start: 0.7541 (p0) cc_final: 0.7133 (p0) REVERT: C 901 MET cc_start: 0.6738 (mmm) cc_final: 0.5147 (mtt) REVERT: C 920 ARG cc_start: 0.6960 (ptt180) cc_final: 0.6607 (ttp-170) REVERT: C 1083 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7812 (ttmt) REVERT: C 1251 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6681 (p-80) REVERT: C 1287 MET cc_start: 0.6434 (pmm) cc_final: 0.5546 (mmt) REVERT: C 1351 VAL cc_start: 0.4579 (OUTLIER) cc_final: 0.4183 (p) REVERT: D 116 TRP cc_start: 0.7306 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: D 238 TRP cc_start: 0.7364 (m-10) cc_final: 0.6528 (m-90) REVERT: D 239 MET cc_start: 0.6857 (ttt) cc_final: 0.6529 (tpt) REVERT: D 254 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.4158 (mp) REVERT: D 288 ARG cc_start: 0.8287 (ptp-110) cc_final: 0.8029 (mtp85) REVERT: D 310 ASP cc_start: 0.8322 (t0) cc_final: 0.8059 (t0) REVERT: D 401 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7484 (ptm-80) REVERT: D 404 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7885 (mm-30) REVERT: D 421 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.4297 (t70) REVERT: D 550 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8661 (mp) REVERT: D 711 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7361 (mpt180) REVERT: D 720 MET cc_start: 0.7442 (mmm) cc_final: 0.7106 (mmm) REVERT: D 730 GLN cc_start: 0.7562 (mt0) cc_final: 0.7115 (tp40) REVERT: D 785 LYS cc_start: 0.8871 (mttp) cc_final: 0.8560 (mttp) REVERT: D 1143 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6254 (p0) REVERT: D 1150 MET cc_start: 0.6585 (tmm) cc_final: 0.5699 (tmm) REVERT: D 1155 GLU cc_start: 0.7986 (pt0) cc_final: 0.7619 (pp20) REVERT: F 520 GLU cc_start: 0.7253 (pm20) cc_final: 0.6878 (pm20) REVERT: Q 211 MET cc_start: 0.3595 (tpt) cc_final: -0.0556 (ptp) REVERT: Q 261 ARG cc_start: 0.7275 (mmp80) cc_final: 0.6935 (ptt-90) REVERT: R 14 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5917 (mmt90) REVERT: R 21 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: R 42 MET cc_start: 0.8929 (mmt) cc_final: 0.8600 (mmm) REVERT: R 74 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6413 (m-10) REVERT: R 287 MET cc_start: 0.4717 (mmm) cc_final: 0.4182 (mmm) outliers start: 122 outliers final: 87 residues processed: 604 average time/residue: 0.2307 time to fit residues: 225.1488 Evaluate side-chains 617 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 516 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain A residue 119 GLU 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 51 LEU 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 B residue 223 LEU Chi-restraints excluded: chain C residue 141 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 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 417 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 519 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 707 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 1066 LYS Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1149 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 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 1323 VAL Chi-restraints excluded: chain C residue 1351 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 76 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 319 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 421 HIS 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 654 VAL Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 765 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 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 1297 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 468 THR 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 548 THR Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET 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 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 151 LEU 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: 0.3980 chunk 357 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 402 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 626 GLN ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1271 GLN C1278 GLN D 158 HIS ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.253031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.179835 restraints weight = 40252.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181318 restraints weight = 23902.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.185310 restraints weight = 14935.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.187592 restraints weight = 9938.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.187994 restraints weight = 8074.535| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36541 Z= 0.142 Angle : 0.648 12.318 50022 Z= 0.329 Chirality : 0.043 0.457 5783 Planarity : 0.005 0.117 6142 Dihedral : 16.179 177.301 6081 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.36 % Allowed : 21.72 % Favored : 73.93 % 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: -1.35 (0.13), residues: 4397 helix: 0.48 (0.13), residues: 1666 sheet: -0.51 (0.26), residues: 404 loop : -2.09 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1345 TYR 0.019 0.002 TYR C 472 PHE 0.041 0.001 PHE R 295 TRP 0.022 0.001 TRP D 34 HIS 0.010 0.001 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (36535) covalent geometry : angle 0.64552 / 0.33 (50016) hydrogen bonds : bond 0.03906 / 2.67 ( 1390) hydrogen bonds : angle 4.70386 / 3.24 ( 3876) metal coordination : bond 0.01137 / 0.48 ( 6) metal coordination : angle 5.59217 / 2.99 ( 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 664 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 518 time to evaluate : 1.313 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: A 28 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.6787 (mmm-85) REVERT: B 4 ARG cc_start: 0.7482 (tpt90) cc_final: 0.7200 (tpt90) REVERT: B 51 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6730 (mp) REVERT: B 200 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3214 (mt) REVERT: C 148 GLU cc_start: 0.7532 (pt0) cc_final: 0.6038 (mt-10) REVERT: C 230 PHE cc_start: 0.7958 (m-80) cc_final: 0.7522 (m-10) REVERT: C 356 ARG cc_start: 0.7320 (tmt170) cc_final: 0.6628 (ttp80) REVERT: C 392 MET cc_start: 0.6894 (tpt) cc_final: 0.6562 (tpt) REVERT: C 532 ILE cc_start: 0.8600 (tp) cc_final: 0.8215 (tp) REVERT: C 660 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4827 (ppp) REVERT: C 692 MET cc_start: 0.7466 (mtm) cc_final: 0.7192 (mtm) REVERT: C 732 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 817 ASN cc_start: 0.7645 (p0) cc_final: 0.7218 (p0) REVERT: C 901 MET cc_start: 0.6873 (mmm) cc_final: 0.5229 (mtt) REVERT: C 920 ARG cc_start: 0.6993 (ptt180) cc_final: 0.6657 (ttp-170) REVERT: C 1251 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6595 (p-80) REVERT: C 1260 ARG cc_start: 0.8063 (ttt-90) cc_final: 0.6913 (ttt-90) REVERT: C 1287 MET cc_start: 0.6261 (pmm) cc_final: 0.5377 (mmt) REVERT: C 1351 VAL cc_start: 0.4605 (OUTLIER) cc_final: 0.4278 (p) REVERT: D 91 VAL cc_start: 0.5148 (OUTLIER) cc_final: 0.4495 (p) REVERT: D 116 TRP cc_start: 0.7342 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: D 239 MET cc_start: 0.6945 (ttt) cc_final: 0.6604 (tpt) REVERT: D 288 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.8065 (mtp85) REVERT: D 310 ASP cc_start: 0.8371 (t0) cc_final: 0.8134 (t0) REVERT: D 401 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7518 (ptm-80) REVERT: D 402 MET cc_start: 0.8143 (mtm) cc_final: 0.7940 (ttm) REVERT: D 404 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7922 (mm-30) REVERT: D 421 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5608 (t70) REVERT: D 550 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8638 (mp) REVERT: D 720 MET cc_start: 0.7343 (mmm) cc_final: 0.7089 (mmm) REVERT: D 730 GLN cc_start: 0.7554 (mt0) cc_final: 0.7120 (tp40) REVERT: D 785 LYS cc_start: 0.8872 (mttp) cc_final: 0.8554 (mttp) REVERT: D 1143 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6284 (p0) REVERT: D 1155 GLU cc_start: 0.8007 (pt0) cc_final: 0.7621 (pp20) REVERT: F 520 GLU cc_start: 0.7272 (pm20) cc_final: 0.6886 (pm20) REVERT: Q 211 MET cc_start: 0.3739 (tpt) cc_final: -0.0369 (ptp) REVERT: Q 261 ARG cc_start: 0.7392 (mmp80) cc_final: 0.7013 (ptt-90) REVERT: R 14 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.5763 (mmt90) REVERT: R 21 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: R 42 MET cc_start: 0.8916 (mmt) cc_final: 0.8647 (mmm) REVERT: R 74 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6159 (m-10) outliers start: 146 outliers final: 107 residues processed: 607 average time/residue: 0.2366 time to fit residues: 231.7720 Evaluate side-chains 627 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 506 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER 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 141 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 210 LEU Chi-restraints excluded: chain C residue 216 LEU 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 417 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL 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 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 828 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1066 LYS Chi-restraints excluded: chain C residue 1106 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 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 1351 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 196 LEU 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 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 401 ARG 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 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 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 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 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 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 548 THR Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET 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 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 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: 0.8980 chunk 81 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 368 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 376 optimal weight: 30.0000 chunk 365 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN ** 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** ** C1090 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.247981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174917 restraints weight = 40283.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.176498 restraints weight = 24500.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.181197 restraints weight = 14698.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183123 restraints weight = 9765.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183322 restraints weight = 8425.065| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36541 Z= 0.201 Angle : 0.718 13.541 50022 Z= 0.367 Chirality : 0.045 0.261 5783 Planarity : 0.005 0.091 6142 Dihedral : 16.278 177.527 6081 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.53 % Allowed : 22.52 % Favored : 72.94 % 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: -1.57 (0.12), residues: 4397 helix: 0.31 (0.13), residues: 1661 sheet: -0.61 (0.26), residues: 402 loop : -2.23 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1345 TYR 0.026 0.002 TYR C 472 PHE 0.040 0.002 PHE R 295 TRP 0.030 0.002 TRP D 34 HIS 0.008 0.001 HIS C1251 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (36535) covalent geometry : angle 0.71419 / 0.37 (50016) hydrogen bonds : bond 0.04366 / 3.00 ( 1390) hydrogen bonds : angle 4.94867 / 3.42 ( 3876) metal coordination : bond 0.01514 / 0.63 ( 6) metal coordination : angle 6.44382 / 3.49 ( 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 671 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 519 time to evaluate : 1.319 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: 0.7489 (mmm-85) cc_final: 0.6876 (mmm-85) REVERT: B 4 ARG cc_start: 0.7586 (tpt90) cc_final: 0.6993 (tpt90) REVERT: B 51 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6830 (mp) REVERT: B 96 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6496 (p-80) REVERT: B 200 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.3573 (mt) REVERT: C 230 PHE cc_start: 0.8081 (m-80) cc_final: 0.7687 (m-80) REVERT: C 294 LEU cc_start: -0.3177 (OUTLIER) cc_final: -0.3389 (pp) REVERT: C 356 ARG cc_start: 0.7346 (tmt170) cc_final: 0.6679 (ttp80) REVERT: C 660 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4801 (ppp) REVERT: C 692 MET cc_start: 0.7477 (mtm) cc_final: 0.7241 (mtm) REVERT: C 701 GLN cc_start: 0.7532 (tt0) cc_final: 0.6927 (tm-30) REVERT: C 732 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7134 (mt-10) REVERT: C 759 MET cc_start: 0.8271 (mmt) cc_final: 0.7936 (mmt) REVERT: C 901 MET cc_start: 0.6955 (mmm) cc_final: 0.5215 (mtt) REVERT: C 1164 GLU cc_start: 0.8081 (pt0) cc_final: 0.7867 (pt0) REVERT: C 1251 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6570 (p-80) REVERT: C 1287 MET cc_start: 0.6589 (pmm) cc_final: 0.5744 (mmt) REVERT: D 91 VAL cc_start: 0.4913 (OUTLIER) cc_final: 0.4172 (p) REVERT: D 116 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: D 131 MET cc_start: 0.7663 (ppp) cc_final: 0.7156 (ppp) REVERT: D 239 MET cc_start: 0.6861 (ttt) cc_final: 0.6589 (tpt) REVERT: D 288 ARG cc_start: 0.8477 (ptp-110) cc_final: 0.8260 (mtp85) REVERT: D 310 ASP cc_start: 0.8505 (t0) cc_final: 0.8268 (t0) REVERT: D 401 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7515 (ptm-80) REVERT: D 404 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7851 (mm-30) REVERT: D 421 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.5962 (t70) REVERT: D 433 ARG cc_start: 0.7376 (tpt170) cc_final: 0.7173 (tpt170) REVERT: D 486 MET cc_start: 0.6782 (ptp) cc_final: 0.6475 (ptp) REVERT: D 550 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8688 (mp) REVERT: D 720 MET cc_start: 0.7213 (mmm) cc_final: 0.6934 (mmm) REVERT: D 730 GLN cc_start: 0.7584 (mt0) cc_final: 0.7138 (tp40) REVERT: D 785 LYS cc_start: 0.8875 (mttp) cc_final: 0.8464 (mmtp) REVERT: D 1143 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6463 (p0) REVERT: F 417 GLU cc_start: 0.7998 (tp30) cc_final: 0.7689 (mm-30) REVERT: F 520 GLU cc_start: 0.7254 (pm20) cc_final: 0.6838 (pm20) REVERT: Q 211 MET cc_start: 0.3936 (tpt) cc_final: -0.0245 (ptp) REVERT: Q 261 ARG cc_start: 0.7422 (mmp80) cc_final: 0.6997 (ptt-90) REVERT: R 14 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.5646 (mmt90) REVERT: R 21 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: R 42 MET cc_start: 0.8963 (mmt) cc_final: 0.8596 (mmt) REVERT: R 74 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6486 (m-10) outliers start: 152 outliers final: 117 residues processed: 615 average time/residue: 0.2381 time to fit residues: 236.8802 Evaluate side-chains 633 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 501 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 114 THR 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 51 LEU 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 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 141 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 294 LEU 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 428 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 519 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 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 828 ILE Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 863 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 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 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 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 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 374 MET Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 401 ARG 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 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 764 THR Chi-restraints excluded: chain D residue 765 VAL 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 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 495 MET 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 579 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET 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 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 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: 0.0370 chunk 283 optimal weight: 9.9990 chunk 190 optimal weight: 0.3980 chunk 219 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 422 optimal weight: 0.0870 chunk 259 optimal weight: 2.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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** C1278 GLN C1302 GLN D 409 GLN D 437 GLN D 680 ASN D 702 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.254301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.178865 restraints weight = 39870.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.181695 restraints weight = 24452.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.186750 restraints weight = 14086.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.189947 restraints weight = 9174.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189806 restraints weight = 7538.976| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36541 Z= 0.123 Angle : 0.654 14.830 50022 Z= 0.330 Chirality : 0.043 0.291 5783 Planarity : 0.005 0.094 6142 Dihedral : 16.213 177.850 6081 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.40 % Allowed : 23.72 % Favored : 72.88 % 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: -1.32 (0.13), residues: 4397 helix: 0.51 (0.13), residues: 1666 sheet: -0.50 (0.26), residues: 391 loop : -2.06 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1345 TYR 0.016 0.001 TYR C 403 PHE 0.049 0.001 PHE R 295 TRP 0.025 0.001 TRP D 238 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (36535) covalent geometry : angle 0.65150 / 0.33 (50016) hydrogen bonds : bond 0.03760 / 2.57 ( 1390) hydrogen bonds : angle 4.60734 / 3.17 ( 3876) metal coordination : bond 0.00990 / 0.45 ( 6) metal coordination : angle 4.71948 / 2.48 ( 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 643 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 529 time to evaluate : 1.003 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: 0.7487 (mmm-85) cc_final: 0.6920 (mmm-85) REVERT: B 4 ARG cc_start: 0.7426 (tpt90) cc_final: 0.6878 (tpt90) REVERT: B 51 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6742 (mp) REVERT: B 200 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3281 (mt) REVERT: B 298 ARG cc_start: 0.4478 (ttp-170) cc_final: 0.4042 (ptm160) REVERT: C 148 GLU cc_start: 0.7234 (pt0) cc_final: 0.5708 (mt-10) REVERT: C 201 TYR cc_start: 0.6838 (m-10) cc_final: 0.6511 (m-10) REVERT: C 230 PHE cc_start: 0.7965 (m-80) cc_final: 0.7567 (m-10) REVERT: C 660 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4713 (ppp) REVERT: C 732 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 817 ASN cc_start: 0.7300 (p0) cc_final: 0.6876 (p0) REVERT: C 901 MET cc_start: 0.6946 (mmm) cc_final: 0.5178 (mtt) REVERT: C 1164 GLU cc_start: 0.8010 (pt0) cc_final: 0.7795 (pt0) REVERT: C 1251 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6479 (p-80) REVERT: C 1287 MET cc_start: 0.6234 (pmm) cc_final: 0.5374 (mmt) REVERT: D 91 VAL cc_start: 0.5090 (OUTLIER) cc_final: 0.4425 (p) REVERT: D 116 TRP cc_start: 0.7281 (OUTLIER) cc_final: 0.6646 (m-10) REVERT: D 239 MET cc_start: 0.6883 (ttt) cc_final: 0.6464 (tpt) REVERT: D 288 ARG cc_start: 0.8292 (ptp-110) cc_final: 0.8024 (mtp85) REVERT: D 310 ASP cc_start: 0.8355 (t0) cc_final: 0.7964 (t0) REVERT: D 401 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (ptm-80) REVERT: D 404 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 421 HIS cc_start: 0.6251 (OUTLIER) cc_final: 0.5601 (t70) REVERT: D 550 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8636 (mp) REVERT: D 720 MET cc_start: 0.7466 (mmm) cc_final: 0.7219 (mmm) REVERT: D 730 GLN cc_start: 0.7394 (mt0) cc_final: 0.7060 (tp40) REVERT: D 785 LYS cc_start: 0.8862 (mttp) cc_final: 0.8400 (mmtp) REVERT: D 1143 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6365 (p0) REVERT: F 417 GLU cc_start: 0.7984 (tp30) cc_final: 0.7593 (mm-30) REVERT: F 520 GLU cc_start: 0.7268 (pm20) cc_final: 0.6946 (pm20) REVERT: Q 211 MET cc_start: 0.3804 (tpt) cc_final: -0.0239 (ptp) REVERT: Q 261 ARG cc_start: 0.7412 (mmp80) cc_final: 0.6955 (ptt-90) REVERT: R 14 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5601 (mmt90) REVERT: R 23 LEU cc_start: 0.6776 (pp) cc_final: 0.6319 (mt) REVERT: R 42 MET cc_start: 0.8995 (mmt) cc_final: 0.8622 (mmt) REVERT: R 74 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6511 (m-10) outliers start: 114 outliers final: 87 residues processed: 596 average time/residue: 0.2135 time to fit residues: 204.7014 Evaluate side-chains 613 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 514 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER 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 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 221 MET Chi-restraints excluded: chain C residue 294 LEU 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 428 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 519 LEU 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 660 MET Chi-restraints excluded: chain C residue 707 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 843 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1149 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 1268 VAL 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 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 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 329 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 401 ARG 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 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 764 THR 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 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 455 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 324 optimal weight: 0.0370 chunk 25 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 314 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 440 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 335 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN D 158 HIS D 432 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.253046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177267 restraints weight = 40280.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.180288 restraints weight = 24696.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.184857 restraints weight = 14597.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.187444 restraints weight = 9654.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.187512 restraints weight = 7807.460| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36541 Z= 0.140 Angle : 0.677 15.427 50022 Z= 0.341 Chirality : 0.043 0.280 5783 Planarity : 0.005 0.080 6142 Dihedral : 16.232 178.514 6081 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.22 % Allowed : 24.22 % Favored : 72.55 % 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: -1.34 (0.13), residues: 4397 helix: 0.50 (0.13), residues: 1660 sheet: -0.53 (0.26), residues: 391 loop : -2.08 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1345 TYR 0.018 0.001 TYR A 176 PHE 0.052 0.001 PHE R 295 TRP 0.024 0.001 TRP D 34 HIS 0.009 0.001 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (36535) covalent geometry : angle 0.67462 / 0.34 (50016) hydrogen bonds : bond 0.03864 / 2.65 ( 1390) hydrogen bonds : angle 4.62405 / 3.18 ( 3876) metal coordination : bond 0.01095 / 0.48 ( 6) metal coordination : angle 4.94513 / 2.65 ( 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 629 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 521 time to evaluate : 1.307 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: A 28 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.6928 (mmm-85) REVERT: B 4 ARG cc_start: 0.7480 (tpt90) cc_final: 0.7229 (tpt90) REVERT: B 51 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6757 (mp) REVERT: B 200 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.3612 (mt) REVERT: C 148 GLU cc_start: 0.7465 (pt0) cc_final: 0.6020 (mt-10) REVERT: C 230 PHE cc_start: 0.7969 (m-80) cc_final: 0.7561 (m-10) REVERT: C 660 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4649 (ppp) REVERT: C 817 ASN cc_start: 0.7435 (p0) cc_final: 0.7145 (p0) REVERT: C 901 MET cc_start: 0.7060 (mmm) cc_final: 0.5253 (mtt) REVERT: C 1164 GLU cc_start: 0.8025 (pt0) cc_final: 0.7818 (pt0) REVERT: C 1251 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6336 (p-80) REVERT: C 1287 MET cc_start: 0.6348 (pmm) cc_final: 0.5557 (mmt) REVERT: D 91 VAL cc_start: 0.5134 (OUTLIER) cc_final: 0.4475 (p) REVERT: D 116 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: D 239 MET cc_start: 0.6955 (ttt) cc_final: 0.6538 (tpt) REVERT: D 310 ASP cc_start: 0.8391 (t0) cc_final: 0.8012 (t0) REVERT: D 401 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7374 (ptm-80) REVERT: D 402 MET cc_start: 0.8189 (mtm) cc_final: 0.7988 (ttm) REVERT: D 404 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7770 (mm-30) REVERT: D 421 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5710 (t70) REVERT: D 486 MET cc_start: 0.6741 (ptp) cc_final: 0.6485 (ptp) REVERT: D 550 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8641 (mp) REVERT: D 720 MET cc_start: 0.7460 (mmm) cc_final: 0.7193 (mmm) REVERT: D 730 GLN cc_start: 0.7465 (mt0) cc_final: 0.7121 (tp40) REVERT: D 1143 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6455 (p0) REVERT: D 1155 GLU cc_start: 0.8008 (pt0) cc_final: 0.7663 (pp20) REVERT: F 520 GLU cc_start: 0.7382 (pm20) cc_final: 0.6956 (pm20) REVERT: Q 211 MET cc_start: 0.3821 (tpt) cc_final: -0.0285 (ptm) REVERT: Q 261 ARG cc_start: 0.7416 (mmp80) cc_final: 0.6948 (ptt-90) REVERT: R 14 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.5063 (mmt90) REVERT: R 42 MET cc_start: 0.8992 (mmt) cc_final: 0.8631 (mmt) REVERT: R 74 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6583 (m-10) outliers start: 108 outliers final: 94 residues processed: 587 average time/residue: 0.2465 time to fit residues: 233.3010 Evaluate side-chains 619 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 513 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 177 SER 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 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 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 417 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 519 LEU 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 660 MET Chi-restraints excluded: chain C residue 707 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 843 GLU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1066 LYS Chi-restraints excluded: chain C residue 1082 ASP Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1149 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 1268 VAL 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 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 158 HIS 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 329 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 VAL 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 645 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 764 THR 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 455 VAL Chi-restraints excluded: chain F residue 471 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 536 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain Q residue 42 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 28 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 363 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 408 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 125 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1278 GLN D 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.254148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178143 restraints weight = 40047.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.179534 restraints weight = 24347.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.184659 restraints weight = 17103.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.189146 restraints weight = 10252.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.189145 restraints weight = 7707.441| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36541 Z= 0.127 Angle : 0.667 14.712 50022 Z= 0.334 Chirality : 0.043 0.344 5783 Planarity : 0.005 0.067 6142 Dihedral : 16.241 179.034 6081 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.34 % Allowed : 24.31 % Favored : 72.34 % 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: -1.30 (0.13), residues: 4397 helix: 0.57 (0.13), residues: 1652 sheet: -0.53 (0.26), residues: 389 loop : -2.07 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1345 TYR 0.032 0.001 TYR C 201 PHE 0.058 0.001 PHE R 295 TRP 0.024 0.001 TRP D 238 HIS 0.041 0.001 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (36535) covalent geometry : angle 0.66479 / 0.33 (50016) hydrogen bonds : bond 0.03736 / 2.56 ( 1390) hydrogen bonds : angle 4.55224 / 3.13 ( 3876) metal coordination : bond 0.01000 / 0.45 ( 6) metal coordination : angle 4.54332 / 2.41 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7427.59 seconds wall clock time: 128 minutes 10.93 seconds (7690.93 seconds total)