Starting phenix.real_space_refine on Fri Mar 6 03:42:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.map" model { file = "/net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wvk_21921/03_2026/6wvk_21921.cif" } resolution = 3.36 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 ------------------------------------------------------------------------------- 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= 0.032 sd= 0.735 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 111 5.16 5 C 17860 2.51 5 N 4911 2.21 5 O 5342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28227 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1642 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8586 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1046} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9149 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1131} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6121 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 21, 'TRANS': 748} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 145 Planarities with less than four sites: {'GLU:plan': 18, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 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 12348 SG CYS D 60 106.742 91.968 125.314 1.00 92.14 S ATOM 12364 SG CYS D 62 106.620 92.720 129.000 1.00 95.34 S ATOM 12472 SG CYS D 75 108.883 90.219 127.771 1.00 94.52 S ATOM 12497 SG CYS D 78 105.310 89.291 127.719 1.00 96.44 S ATOM 18268 SG CYS D 818 105.030 63.256 68.256 1.00 34.15 S ATOM 18853 SG CYS D 892 102.544 65.836 69.059 1.00 31.53 S ATOM 18902 SG CYS D 899 105.985 66.838 67.948 1.00 28.13 S ATOM 18928 SG CYS D 902 103.757 65.438 65.798 1.00 27.15 S Time building chain proxies: 5.03, per 1000 atoms: 0.18 Number of scatterers: 28227 At special positions: 0 Unit cell: (151.2, 168.84, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 111 16.00 Mg 1 11.99 O 5342 8.00 N 4911 7.00 C 17860 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: 2.26 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 902 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 818 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 899 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 892 " Number of angles added : 12 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 44 sheets defined 40.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.687A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.813A pdb=" N ASN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 226 removed outlier: 3.635A pdb=" N ILE A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.503A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.789A pdb=" N LEU B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 205 through 221 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.570A pdb=" N THR C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 191 through 199 removed outlier: 4.250A pdb=" N LEU C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 4.160A pdb=" N ASP C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.612A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.750A pdb=" N PHE C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 392 removed outlier: 3.579A pdb=" N ILE C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 435 removed outlier: 3.861A pdb=" N GLY C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 451 through 465 removed outlier: 4.419A pdb=" N SER C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.696A pdb=" N LYS C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.604A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.606A pdb=" N ASN C 571 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 3.591A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.716A pdb=" N CYS C 625 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 626 " --> pdb=" O THR C 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 626' Processing helix chain 'C' and resid 628 through 632 removed outlier: 3.737A pdb=" N ASN C 631 " --> pdb=" O PHE C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.937A pdb=" N MET C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 removed outlier: 4.636A pdb=" N VAL C 665 " --> pdb=" O GLY C 661 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY C 671 " --> pdb=" O GLY C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 698 Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 967 through 984 removed outlier: 4.035A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 974 " --> pdb=" O GLN C 970 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 975 " --> pdb=" O VAL C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 removed outlier: 3.695A pdb=" N GLU C1002 " --> pdb=" O GLU C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1047 Processing helix chain 'C' and resid 1077 through 1087 Processing helix chain 'C' and resid 1088 through 1098 removed outlier: 3.515A pdb=" N LEU C1092 " --> pdb=" O ALA C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1116 Processing helix chain 'C' and resid 1125 through 1137 removed outlier: 4.250A pdb=" N LYS C1129 " --> pdb=" O PRO C1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.849A pdb=" N GLU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.899A pdb=" N LYS D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.709A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.641A pdb=" N GLU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 219 removed outlier: 3.754A pdb=" N VAL D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 275 removed outlier: 4.280A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 removed outlier: 4.422A pdb=" N ASN D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.566A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 397 through 405 removed outlier: 4.038A pdb=" N GLU D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.762A pdb=" N VAL D 442 " --> pdb=" O HIS D 439 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS D 443 " --> pdb=" O PRO D 440 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 444' Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 493 through 504 Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 550 through 555 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 616 through 631 Processing helix chain 'D' and resid 632 through 655 removed outlier: 4.003A pdb=" N ASP D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 642 " --> pdb=" O LYS D 638 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY D 655 " --> pdb=" O SER D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 690 removed outlier: 3.915A pdb=" N GLU D 674 " --> pdb=" O GLN D 670 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU D 675 " --> pdb=" O GLU D 671 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 678 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 680 " --> pdb=" O ALA D 676 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP D 681 " --> pdb=" O GLN D 677 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN D 682 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 685 " --> pdb=" O ASP D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 720 removed outlier: 3.710A pdb=" N GLU D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 709 " --> pdb=" O TRP D 705 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS D 718 " --> pdb=" O GLY D 714 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 removed outlier: 3.614A pdb=" N SER D 730 " --> pdb=" O ILE D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 746 removed outlier: 3.967A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 779 Processing helix chain 'D' and resid 787 through 794 Processing helix chain 'D' and resid 798 through 809 Processing helix chain 'D' and resid 839 through 844 removed outlier: 3.502A pdb=" N LEU D 843 " --> pdb=" O LEU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 4.841A pdb=" N GLU D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 879 " --> pdb=" O GLU D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.518A pdb=" N THR D 891 " --> pdb=" O SER D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 904 Processing helix chain 'D' and resid 918 through 938 Proline residue: D 930 - end of helix Processing helix chain 'D' and resid 942 through 946 removed outlier: 3.692A pdb=" N ALA D 945 " --> pdb=" O GLY D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 960 removed outlier: 3.619A pdb=" N GLU D 958 " --> pdb=" O PRO D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1038 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 3.718A pdb=" N GLU D1045 " --> pdb=" O THR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1072 removed outlier: 3.957A pdb=" N VAL D1067 " --> pdb=" O GLY D1063 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D1070 " --> pdb=" O HIS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1075 No H-bonds generated for 'chain 'D' and resid 1073 through 1075' Processing helix chain 'D' and resid 1096 through 1104 removed outlier: 3.706A pdb=" N ALA D1102 " --> pdb=" O GLN D1098 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 3.955A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1153 removed outlier: 3.815A pdb=" N ASP D1148 " --> pdb=" O ARG D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1168 removed outlier: 3.832A pdb=" N ASN D1164 " --> pdb=" O GLY D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1176 Processing helix chain 'D' and resid 1177 through 1182 Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 15 through 33 removed outlier: 3.504A pdb=" N GLU F 29 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.581A pdb=" N LEU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 51 removed outlier: 3.657A pdb=" N LYS H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 42 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP H 50 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 98 removed outlier: 3.630A pdb=" N ALA H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS H 97 " --> pdb=" O HIS H 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 145 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 201 through 222 removed outlier: 4.614A pdb=" N LYS H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 254 removed outlier: 3.604A pdb=" N ALA H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 280 removed outlier: 4.527A pdb=" N SER H 274 " --> pdb=" O PHE H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 301 removed outlier: 3.524A pdb=" N HIS H 299 " --> pdb=" O GLU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 319 removed outlier: 3.590A pdb=" N GLU H 315 " --> pdb=" O PHE H 311 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR H 316 " --> pdb=" O ASP H 312 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 341 through 353 removed outlier: 3.572A pdb=" N SER H 353 " --> pdb=" O VAL H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 382 removed outlier: 3.740A pdb=" N ILE H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR H 380 " --> pdb=" O GLN H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 407 removed outlier: 3.764A pdb=" N TRP H 398 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER H 401 " --> pdb=" O LYS H 397 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS H 405 " --> pdb=" O SER H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 413 removed outlier: 3.919A pdb=" N ARG H 412 " --> pdb=" O LYS H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 424 through 439 removed outlier: 4.753A pdb=" N GLU H 437 " --> pdb=" O LYS H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 474 Proline residue: H 467 - end of helix Processing helix chain 'H' and resid 479 through 486 Processing helix chain 'H' and resid 499 through 514 removed outlier: 4.412A pdb=" N ILE H 503 " --> pdb=" O LYS H 499 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY H 504 " --> pdb=" O MET H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 519 No H-bonds generated for 'chain 'H' and resid 517 through 519' Processing helix chain 'H' and resid 520 through 533 removed outlier: 3.700A pdb=" N PHE H 524 " --> pdb=" O ASP H 520 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU H 525 " --> pdb=" O ALA H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 563 removed outlier: 3.559A pdb=" N MET H 556 " --> pdb=" O SER H 552 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA H 557 " --> pdb=" O PRO H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 577 Processing helix chain 'H' and resid 610 through 621 removed outlier: 5.070A pdb=" N PHE H 616 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR H 617 " --> pdb=" O ILE H 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 619 " --> pdb=" O GLU H 615 " (cutoff:3.500A) Processing helix chain 'H' and resid 646 through 651 Processing helix chain 'H' and resid 652 through 657 Processing helix chain 'H' and resid 657 through 663 Processing helix chain 'H' and resid 673 through 685 removed outlier: 4.072A pdb=" N GLN H 679 " --> pdb=" O HIS H 675 " (cutoff:3.500A) Processing helix chain 'H' and resid 708 through 713 Processing helix chain 'H' and resid 735 through 744 removed outlier: 4.361A pdb=" N LEU H 739 " --> pdb=" O ASP H 735 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 765 removed outlier: 3.816A pdb=" N THR H 763 " --> pdb=" O SER H 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.731A pdb=" N LYS A 22 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 189 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG A 184 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR A 191 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A 182 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 193 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 180 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 195 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 197 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 176 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TRP A 199 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 7.638A pdb=" N ARG A 137 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 58 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE A 56 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.582A pdb=" N ALA A 128 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 5.906A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG B 175 " --> pdb=" O TRP B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 101 removed outlier: 8.090A pdb=" N ARG B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE B 58 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 143 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB1, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 removed outlier: 7.544A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 62 through 71 removed outlier: 6.365A pdb=" N LYS C 95 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR C 69 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 93 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 92 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE C 112 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL C 94 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP C 110 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 96 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AB5, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.567A pdb=" N SER C 136 " --> pdb=" O ARG C 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 148 removed outlier: 5.683A pdb=" N PHE C 158 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR C 174 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 170 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 350 Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 7.248A pdb=" N ILE C 543 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU C 564 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR C 545 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP C 562 " --> pdb=" O THR C 545 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR C 547 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG C 560 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 549 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 675 removed outlier: 6.407A pdb=" N VAL C 674 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 707 through 711 removed outlier: 6.743A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 763 removed outlier: 9.115A pdb=" N ILE C 955 " --> pdb=" O ASN C 758 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET C 760 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 957 " --> pdb=" O MET C 760 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY C 762 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 927 " --> pdb=" O ASN C 931 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 800 removed outlier: 6.520A pdb=" N SER C 789 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 916 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS C 791 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 914 " --> pdb=" O HIS C 791 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 793 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR C 912 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 795 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG C 910 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER C 797 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C 908 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 799 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN C 906 " --> pdb=" O ASN C 894 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN C 894 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 908 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 892 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 910 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL C 890 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR C 912 " --> pdb=" O HIS C 888 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 841 through 847 removed outlier: 3.658A pdb=" N VAL C 843 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 875 " --> pdb=" O LYS C 845 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 847 " --> pdb=" O ARG C 873 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1073 through 1075 Processing sheet with id=AD1, first strand: chain 'C' and resid 1140 through 1145 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.468A pdb=" N HIS D 94 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP D 229 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N ALA D 99 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N ILE D 227 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 135 through 138 removed outlier: 6.682A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 339 through 346 Processing sheet with id=AD5, first strand: chain 'D' and resid 515 through 516 removed outlier: 3.714A pdb=" N LEU D 557 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 752 through 753 Processing sheet with id=AD7, first strand: chain 'D' and resid 812 through 815 Processing sheet with id=AD8, first strand: chain 'D' and resid 824 through 826 removed outlier: 3.524A pdb=" N VAL D 884 " --> pdb=" O ALA D 826 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 999 through 1005 Processing sheet with id=AE1, first strand: chain 'D' and resid 1093 through 1095 removed outlier: 4.611A pdb=" N LYS D1077 " --> pdb=" O VAL D1119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1185 through 1186 Processing sheet with id=AE3, first strand: chain 'E' and resid 21 through 26 removed outlier: 4.229A pdb=" N ILE E 2 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN E 8 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 44 " --> pdb=" O GLN E 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 135 through 136 removed outlier: 7.424A pdb=" N TYR H 135 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR H 118 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY H 102 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE H 101 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN H 171 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG H 103 " --> pdb=" O LYS H 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 169 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP H 105 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 135 through 136 removed outlier: 7.424A pdb=" N TYR H 135 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR H 118 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY H 102 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE H 101 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN H 171 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG H 103 " --> pdb=" O LYS H 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 169 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP H 105 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN H 171 " --> pdb=" O MET H 182 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET H 182 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET H 173 " --> pdb=" O LYS H 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 289 through 291 removed outlier: 3.799A pdb=" N GLU H 289 " --> pdb=" O ILE H 263 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL H 264 " --> pdb=" O PHE H 544 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASP H 546 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE H 266 " --> pdb=" O ASP H 546 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 229 " --> pdb=" O VAL H 570 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY H 572 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL H 231 " --> pdb=" O GLY H 572 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 5.866A pdb=" N LYS H 306 " --> pdb=" O LEU H 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'H' and resid 691 through 692 removed outlier: 7.079A pdb=" N ARG H 691 " --> pdb=" O VAL H 706 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR H 666 " --> pdb=" O PHE H 717 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP H 718 " --> pdb=" O MET H 747 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET H 749 " --> pdb=" O ASP H 718 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA H 751 " --> pdb=" O VAL H 720 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU H 638 " --> pdb=" O LEU H 750 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL H 639 " --> pdb=" O ALA H 773 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4851 1.31 - 1.43: 7087 1.43 - 1.56: 16588 1.56 - 1.69: 0 1.69 - 1.81: 198 Bond restraints: 28724 Sorted by residual: bond pdb=" C PRO C 262 " pdb=" N LYS C 263 " ideal model delta sigma weight residual 1.334 1.246 0.087 1.30e-02 5.92e+03 4.51e+01 bond pdb=" C LEU C 285 " pdb=" N PHE C 286 " ideal model delta sigma weight residual 1.331 1.266 0.064 1.37e-02 5.33e+03 2.20e+01 bond pdb=" C LYS C 263 " pdb=" O LYS C 263 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.17e-02 7.31e+03 2.11e+01 bond pdb=" N LYS C 263 " pdb=" CA LYS C 263 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.20e-02 6.94e+03 1.54e+01 bond pdb=" CA LYS C 263 " pdb=" C LYS C 263 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.25e-02 6.40e+03 1.48e+01 ... (remaining 28719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 37669 2.17 - 4.34: 1085 4.34 - 6.51: 114 6.51 - 8.68: 10 8.68 - 10.85: 5 Bond angle restraints: 38883 Sorted by residual: angle pdb=" N VAL D 87 " pdb=" CA VAL D 87 " pdb=" C VAL D 87 " ideal model delta sigma weight residual 112.43 104.46 7.97 9.20e-01 1.18e+00 7.51e+01 angle pdb=" N LYS C 263 " pdb=" CA LYS C 263 " pdb=" C LYS C 263 " ideal model delta sigma weight residual 111.24 100.47 10.77 1.29e+00 6.01e-01 6.97e+01 angle pdb=" CA SER D 315 " pdb=" C SER D 315 " pdb=" O SER D 315 " ideal model delta sigma weight residual 117.94 121.83 -3.89 5.80e-01 2.97e+00 4.50e+01 angle pdb=" N LYS C 263 " pdb=" CA LYS C 263 " pdb=" CB LYS C 263 " ideal model delta sigma weight residual 110.07 101.08 8.99 1.47e+00 4.63e-01 3.74e+01 angle pdb=" CA ASP D 451 " pdb=" CB ASP D 451 " pdb=" CG ASP D 451 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 38878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14821 18.05 - 36.09: 1991 36.09 - 54.14: 525 54.14 - 72.18: 89 72.18 - 90.23: 36 Dihedral angle restraints: 17462 sinusoidal: 6981 harmonic: 10481 Sorted by residual: dihedral pdb=" N LYS C 263 " pdb=" C LYS C 263 " pdb=" CA LYS C 263 " pdb=" CB LYS C 263 " ideal model delta harmonic sigma weight residual 122.80 103.62 19.18 0 2.50e+00 1.60e-01 5.89e+01 dihedral pdb=" C LYS C 263 " pdb=" N LYS C 263 " pdb=" CA LYS C 263 " pdb=" CB LYS C 263 " ideal model delta harmonic sigma weight residual -122.60 -103.62 -18.98 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" CA GLY C 212 " pdb=" C GLY C 212 " pdb=" N GLU C 213 " pdb=" CA GLU C 213 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 17459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4051 0.088 - 0.177: 368 0.177 - 0.265: 14 0.265 - 0.353: 0 0.353 - 0.441: 2 Chirality restraints: 4435 Sorted by residual: chirality pdb=" CA LYS C 263 " pdb=" N LYS C 263 " pdb=" C LYS C 263 " pdb=" CB LYS C 263 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ASP D 451 " pdb=" N ASP D 451 " pdb=" C ASP D 451 " pdb=" CB ASP D 451 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA THR C 59 " pdb=" N THR C 59 " pdb=" C THR C 59 " pdb=" CB THR C 59 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4432 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 432 " 0.576 9.50e-02 1.11e+02 2.58e-01 4.14e+01 pdb=" NE ARG C 432 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 432 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 432 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 432 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 32 " 0.058 2.00e-02 2.50e+03 3.86e-02 2.98e+01 pdb=" CG TYR B 32 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR B 32 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 32 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR B 32 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 32 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 32 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 32 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 329 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ARG C 329 " -0.077 2.00e-02 2.50e+03 pdb=" O ARG C 329 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS C 330 " 0.026 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 126 2.45 - 3.06: 18370 3.06 - 3.67: 40732 3.67 - 4.29: 61206 4.29 - 4.90: 103803 Nonbonded interactions: 224237 Sorted by model distance: nonbonded pdb=" O PHE C 328 " pdb=" OH TYR C 332 " model vdw 1.836 3.040 nonbonded pdb=" OD1 ASP D 449 " pdb="MG MG D2001 " model vdw 1.902 2.170 nonbonded pdb=" OD1 ASP D 451 " pdb="MG MG D2001 " model vdw 1.959 2.170 nonbonded pdb=" OD1 ASP D 453 " pdb="MG MG D2001 " model vdw 2.049 2.170 nonbonded pdb=" O HIS H 681 " pdb=" OG SER H 685 " model vdw 2.109 3.040 ... (remaining 224232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 5 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 62 or (resid 63 through 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB )) or resid 70 through \ 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or res \ id 89 through 93 or (resid 94 through 95 and (name N or name CA or name C or nam \ e O or name CB )) or resid 96 through 101 or (resid 102 and (name N or name CA o \ r name C or name O or name CB )) or resid 103 through 131 or (resid 132 through \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throug \ h 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or \ resid 140 through 156 or (resid 157 and (name N or name CA or name C or name O o \ r name CB )) or resid 158 or (resid 159 and (name N or name CA or name C or name \ O or name CB )) or resid 160 through 228)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 28 or (resid 29 and (name N or name CA \ or name C or name O or name CB )) or resid 30 through 228)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.284 28732 Z= 0.289 Angle : 0.850 10.851 38895 Z= 0.523 Chirality : 0.050 0.441 4435 Planarity : 0.006 0.258 5058 Dihedral : 17.758 90.226 10724 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 6.50 % Allowed : 19.09 % Favored : 74.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.74 % 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: -3.37 (0.12), residues: 3611 helix: -2.09 (0.12), residues: 1296 sheet: -1.02 (0.23), residues: 485 loop : -2.72 (0.12), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 432 TYR 0.069 0.002 TYR B 32 PHE 0.048 0.002 PHE B 23 TRP 0.040 0.002 TRP H 8 HIS 0.006 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00551 (28724) covalent geometry : angle 0.84887 (38883) hydrogen bonds : bond 0.13909 ( 1090) hydrogen bonds : angle 6.12195 ( 3108) metal coordination : bond 0.12711 ( 8) metal coordination : angle 2.41291 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 756 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: C 13 GLN cc_start: 0.8659 (pt0) cc_final: 0.8449 (pt0) REVERT: C 42 ASP cc_start: 0.7344 (m-30) cc_final: 0.7117 (m-30) REVERT: C 214 ASN cc_start: 0.6824 (m-40) cc_final: 0.6588 (m-40) REVERT: C 296 ASP cc_start: 0.4791 (m-30) cc_final: 0.4531 (m-30) REVERT: C 572 TYR cc_start: 0.7650 (m-80) cc_final: 0.6541 (m-80) REVERT: C 605 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7021 (ptt90) REVERT: C 607 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5190 (mtm180) REVERT: C 678 HIS cc_start: 0.7941 (m-70) cc_final: 0.7731 (m-70) REVERT: C 973 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: C 981 ARG cc_start: 0.7708 (tmm-80) cc_final: 0.7382 (ttt90) REVERT: C 1004 LEU cc_start: 0.8893 (mp) cc_final: 0.8631 (mp) REVERT: D 35 ASN cc_start: 0.7149 (t0) cc_final: 0.6948 (m-40) REVERT: D 264 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7467 (ttm110) REVERT: D 360 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 544 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7896 (pp) REVERT: D 558 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8482 (tp) REVERT: D 589 LYS cc_start: 0.7041 (ptmm) cc_final: 0.6546 (ptmm) REVERT: D 629 LYS cc_start: 0.8907 (tmmt) cc_final: 0.8366 (ttpp) REVERT: D 748 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7989 (tmt170) REVERT: D 753 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7382 (p0) REVERT: D 769 GLU cc_start: 0.7335 (tt0) cc_final: 0.7065 (tt0) REVERT: D 835 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7652 (t) REVERT: D 837 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7402 (tt0) REVERT: D 844 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8655 (mm) REVERT: D 975 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7887 (p0) REVERT: H 29 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8158 (mp) REVERT: H 103 ARG cc_start: 0.7973 (tmm-80) cc_final: 0.7728 (ttt180) REVERT: H 195 GLN cc_start: 0.6290 (tm130) cc_final: 0.4644 (mt0) REVERT: H 385 ASN cc_start: 0.6231 (p0) cc_final: 0.5911 (p0) REVERT: H 439 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7160 (ttpp) REVERT: H 608 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6776 (mmt-90) REVERT: H 671 CYS cc_start: 0.6632 (p) cc_final: 0.6413 (p) outliers start: 195 outliers final: 138 residues processed: 893 average time/residue: 0.1926 time to fit residues: 265.5171 Evaluate side-chains 871 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 719 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 823 ASN Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 973 GLU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 748 ARG Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 958 GLU Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 974 ILE Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1152 LYS Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 370 ILE Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain H residue 384 GLN Chi-restraints excluded: chain H residue 392 MET Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain H residue 577 SER Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 608 ARG Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 677 CYS Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 ASN C 390 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 HIS ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D 585 ASN D 743 GLN ** D 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS H 214 GLN H 294 GLN H 374 GLN H 454 GLN H 612 GLN H 631 ASN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 679 GLN H 683 HIS H 771 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.161489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.139917 restraints weight = 38674.449| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.07 r_work: 0.3318 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28732 Z= 0.199 Angle : 0.684 11.168 38895 Z= 0.355 Chirality : 0.047 0.202 4435 Planarity : 0.005 0.065 5058 Dihedral : 9.216 61.021 4233 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 5.40 % Allowed : 23.88 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.40 (0.13), residues: 3611 helix: -1.10 (0.14), residues: 1303 sheet: -0.66 (0.24), residues: 460 loop : -2.23 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 694 TYR 0.018 0.002 TYR D 650 PHE 0.037 0.002 PHE H 761 TRP 0.022 0.002 TRP H 8 HIS 0.011 0.001 HIS H 694 Details of bonding type rmsd covalent geometry : bond 0.00466 (28724) covalent geometry : angle 0.67979 (38883) hydrogen bonds : bond 0.05576 ( 1090) hydrogen bonds : angle 5.39124 ( 3108) metal coordination : bond 0.01413 ( 8) metal coordination : angle 4.22565 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 732 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6457 (mt-10) REVERT: A 47 SER cc_start: 0.8602 (m) cc_final: 0.8202 (t) REVERT: A 98 GLU cc_start: 0.6968 (tp30) cc_final: 0.6619 (tp30) REVERT: B 140 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8053 (mt) REVERT: B 144 ARG cc_start: 0.8443 (mtm180) cc_final: 0.8093 (mtm180) REVERT: B 154 ASN cc_start: 0.8076 (m-40) cc_final: 0.7856 (m-40) REVERT: C 42 ASP cc_start: 0.7875 (m-30) cc_final: 0.7620 (m-30) REVERT: C 296 ASP cc_start: 0.4887 (m-30) cc_final: 0.4579 (m-30) REVERT: C 572 TYR cc_start: 0.7850 (m-80) cc_final: 0.6586 (m-80) REVERT: C 589 ASP cc_start: 0.8268 (p0) cc_final: 0.7969 (p0) REVERT: C 605 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.5945 (ptt90) REVERT: C 607 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.5845 (mtm180) REVERT: C 981 ARG cc_start: 0.7903 (tmm-80) cc_final: 0.7602 (ttt90) REVERT: C 1004 LEU cc_start: 0.8795 (mp) cc_final: 0.8531 (mp) REVERT: C 1126 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: D 264 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7502 (ttm110) REVERT: D 287 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7208 (mmp) REVERT: D 360 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7982 (mt-10) REVERT: D 437 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8067 (mtt-85) REVERT: D 629 LYS cc_start: 0.8931 (tmmt) cc_final: 0.8390 (ttpp) REVERT: D 731 ASP cc_start: 0.8603 (t70) cc_final: 0.8403 (t0) REVERT: D 753 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.7236 (p0) REVERT: D 835 THR cc_start: 0.8118 (m) cc_final: 0.7651 (t) REVERT: D 837 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7546 (tt0) REVERT: H 36 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8039 (tt) REVERT: H 87 GLN cc_start: 0.8186 (mp10) cc_final: 0.7856 (mm-40) REVERT: H 103 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.8016 (ttt180) REVERT: H 145 TYR cc_start: 0.8623 (t80) cc_final: 0.8051 (t80) REVERT: H 195 GLN cc_start: 0.6181 (tm130) cc_final: 0.4674 (mt0) REVERT: H 385 ASN cc_start: 0.7061 (p0) cc_final: 0.6612 (p0) REVERT: H 439 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7185 (ttpp) REVERT: H 500 MET cc_start: 0.8119 (tmm) cc_final: 0.7830 (tmm) REVERT: H 543 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8223 (tt) REVERT: H 683 HIS cc_start: 0.6980 (m170) cc_final: 0.6655 (m90) REVERT: H 716 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8208 (mm-30) outliers start: 162 outliers final: 104 residues processed: 835 average time/residue: 0.1900 time to fit residues: 245.5118 Evaluate side-chains 825 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 710 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1117 ASP Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 748 ARG Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 370 ILE Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 721 LEU Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 130 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 68 optimal weight: 0.0870 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 133 ASN B 187 GLN C 137 GLN C 450 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN D 585 ASN D 609 GLN D 743 GLN ** D 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.166034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.144496 restraints weight = 38816.861| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.08 r_work: 0.3374 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28732 Z= 0.118 Angle : 0.597 10.184 38895 Z= 0.308 Chirality : 0.044 0.175 4435 Planarity : 0.004 0.052 5058 Dihedral : 7.783 59.460 4104 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 5.13 % Allowed : 24.88 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.72 (0.13), residues: 3611 helix: -0.44 (0.14), residues: 1293 sheet: -0.34 (0.23), residues: 487 loop : -1.91 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.016 0.001 TYR D 70 PHE 0.039 0.001 PHE H 761 TRP 0.015 0.001 TRP H 8 HIS 0.009 0.001 HIS H 694 Details of bonding type rmsd covalent geometry : bond 0.00259 (28724) covalent geometry : angle 0.59433 (38883) hydrogen bonds : bond 0.04408 ( 1090) hydrogen bonds : angle 5.02117 ( 3108) metal coordination : bond 0.00631 ( 8) metal coordination : angle 2.96766 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 749 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: A 47 SER cc_start: 0.8532 (m) cc_final: 0.8133 (t) REVERT: A 98 GLU cc_start: 0.7024 (tp30) cc_final: 0.6526 (tp30) REVERT: B 140 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8093 (mt) REVERT: B 154 ASN cc_start: 0.8016 (m-40) cc_final: 0.7814 (m-40) REVERT: C 42 ASP cc_start: 0.7851 (m-30) cc_final: 0.7623 (m-30) REVERT: C 82 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7328 (ttmm) REVERT: C 95 LYS cc_start: 0.8025 (tptp) cc_final: 0.7805 (tmtt) REVERT: C 171 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: C 296 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4589 (m-30) REVERT: C 572 TYR cc_start: 0.7895 (m-80) cc_final: 0.6548 (m-80) REVERT: C 597 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7947 (mtm-85) REVERT: C 966 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: C 981 ARG cc_start: 0.7872 (tmm-80) cc_final: 0.7470 (ttt90) REVERT: C 1004 LEU cc_start: 0.8782 (mp) cc_final: 0.8461 (mp) REVERT: C 1097 THR cc_start: 0.8829 (m) cc_final: 0.8498 (p) REVERT: C 1126 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: D 35 ASN cc_start: 0.7234 (m-40) cc_final: 0.7016 (m-40) REVERT: D 260 ARG cc_start: 0.8402 (mpt180) cc_final: 0.7352 (mtp180) REVERT: D 264 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7658 (ttm-80) REVERT: D 274 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7298 (tt) REVERT: D 287 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7374 (mmp) REVERT: D 360 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7977 (mt-10) REVERT: D 437 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8016 (mtt-85) REVERT: D 629 LYS cc_start: 0.8844 (tmmt) cc_final: 0.8359 (ttpp) REVERT: D 731 ASP cc_start: 0.8531 (t70) cc_final: 0.8311 (t0) REVERT: D 769 GLU cc_start: 0.7591 (tt0) cc_final: 0.7319 (tt0) REVERT: D 772 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7192 (p) REVERT: D 835 THR cc_start: 0.8039 (m) cc_final: 0.7538 (t) REVERT: D 837 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7479 (tt0) REVERT: D 934 LEU cc_start: 0.8008 (mt) cc_final: 0.7556 (mp) REVERT: D 1115 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7417 (p) REVERT: E 1 MET cc_start: 0.8518 (tpp) cc_final: 0.8304 (tpt) REVERT: H 7 GLU cc_start: 0.5460 (mp0) cc_final: 0.4846 (mp0) REVERT: H 14 ARG cc_start: 0.7913 (mpt180) cc_final: 0.7535 (tpt-90) REVERT: H 29 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8212 (mp) REVERT: H 36 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7989 (tt) REVERT: H 86 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: H 87 GLN cc_start: 0.8156 (mp10) cc_final: 0.7799 (mm-40) REVERT: H 103 ARG cc_start: 0.8169 (tmm-80) cc_final: 0.7884 (ttt180) REVERT: H 138 ARG cc_start: 0.8309 (mtt90) cc_final: 0.8103 (mtt90) REVERT: H 195 GLN cc_start: 0.6087 (tm130) cc_final: 0.4729 (mt0) REVERT: H 385 ASN cc_start: 0.7068 (p0) cc_final: 0.6603 (p0) REVERT: H 440 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8243 (mtp180) REVERT: H 465 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7077 (t80) REVERT: H 528 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: H 543 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8285 (tt) REVERT: H 615 GLU cc_start: 0.8044 (pt0) cc_final: 0.7842 (pt0) REVERT: H 684 MET cc_start: 0.6905 (tpt) cc_final: 0.6705 (tpt) outliers start: 154 outliers final: 90 residues processed: 839 average time/residue: 0.1901 time to fit residues: 249.0666 Evaluate side-chains 806 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 698 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 370 ILE Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 23 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 187 GLN C 276 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 585 ASN H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN H 205 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 679 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.162623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.141200 restraints weight = 38830.061| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.05 r_work: 0.3335 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28732 Z= 0.192 Angle : 0.639 10.138 38895 Z= 0.329 Chirality : 0.046 0.191 4435 Planarity : 0.005 0.057 5058 Dihedral : 7.172 59.991 4042 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 6.03 % Allowed : 25.52 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.65 (0.13), residues: 3611 helix: -0.35 (0.15), residues: 1303 sheet: -0.36 (0.23), residues: 491 loop : -1.88 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 688 TYR 0.019 0.002 TYR D 650 PHE 0.026 0.002 PHE H 761 TRP 0.013 0.001 TRP H 8 HIS 0.011 0.001 HIS H 683 Details of bonding type rmsd covalent geometry : bond 0.00452 (28724) covalent geometry : angle 0.63601 (38883) hydrogen bonds : bond 0.05075 ( 1090) hydrogen bonds : angle 5.09517 ( 3108) metal coordination : bond 0.01025 ( 8) metal coordination : angle 3.70086 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 716 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8598 (m) cc_final: 0.8147 (t) REVERT: A 84 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8479 (mtmm) REVERT: A 98 GLU cc_start: 0.7041 (tp30) cc_final: 0.6546 (tp30) REVERT: B 140 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8172 (mt) REVERT: C 42 ASP cc_start: 0.7844 (m-30) cc_final: 0.7548 (m-30) REVERT: C 82 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7313 (ttmm) REVERT: C 171 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: C 183 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.7099 (ttt-90) REVERT: C 296 ASP cc_start: 0.4947 (OUTLIER) cc_final: 0.4641 (m-30) REVERT: C 572 TYR cc_start: 0.7904 (m-80) cc_final: 0.6490 (m-80) REVERT: C 597 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8055 (mtm-85) REVERT: C 966 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7973 (mtt) REVERT: C 981 ARG cc_start: 0.7884 (tmm-80) cc_final: 0.7461 (ttt90) REVERT: C 1004 LEU cc_start: 0.8749 (mp) cc_final: 0.8423 (mp) REVERT: C 1097 THR cc_start: 0.8838 (m) cc_final: 0.8487 (p) REVERT: C 1126 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: D 35 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7121 (m-40) REVERT: D 260 ARG cc_start: 0.8516 (mpt180) cc_final: 0.7367 (mtp180) REVERT: D 264 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7677 (ttm110) REVERT: D 274 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7192 (tt) REVERT: D 287 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7331 (mmp) REVERT: D 360 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 437 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8020 (mtt-85) REVERT: D 629 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8485 (ttpp) REVERT: D 637 SER cc_start: 0.9117 (t) cc_final: 0.8658 (m) REVERT: D 748 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8366 (tmt170) REVERT: D 835 THR cc_start: 0.8046 (m) cc_final: 0.7574 (t) REVERT: D 837 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7550 (tt0) REVERT: D 975 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8073 (p0) REVERT: D 1025 THR cc_start: 0.8909 (t) cc_final: 0.8617 (m) REVERT: E 38 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7459 (mttt) REVERT: H 29 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8150 (mp) REVERT: H 36 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8018 (tt) REVERT: H 86 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: H 87 GLN cc_start: 0.8147 (mp10) cc_final: 0.7758 (mm-40) REVERT: H 103 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.8000 (ttt180) REVERT: H 195 GLN cc_start: 0.6225 (tm130) cc_final: 0.4863 (mt0) REVERT: H 385 ASN cc_start: 0.7110 (p0) cc_final: 0.6684 (p0) REVERT: H 465 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7134 (t80) REVERT: H 528 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: H 530 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (tt) REVERT: H 543 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (tt) REVERT: H 684 MET cc_start: 0.6941 (tpt) cc_final: 0.6730 (tpt) outliers start: 181 outliers final: 118 residues processed: 826 average time/residue: 0.1931 time to fit residues: 247.5073 Evaluate side-chains 833 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 695 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 748 ARG Chi-restraints excluded: chain D residue 758 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 354 optimal weight: 8.9990 chunk 335 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 338 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN C 276 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.163027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.141535 restraints weight = 38908.395| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.06 r_work: 0.3343 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28732 Z= 0.172 Angle : 0.625 10.675 38895 Z= 0.321 Chirality : 0.045 0.251 4435 Planarity : 0.004 0.055 5058 Dihedral : 7.014 59.556 4036 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 6.50 % Allowed : 25.25 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.53 (0.13), residues: 3611 helix: -0.25 (0.15), residues: 1304 sheet: -0.23 (0.23), residues: 494 loop : -1.83 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.018 0.001 TYR D 650 PHE 0.032 0.002 PHE H 761 TRP 0.011 0.001 TRP H 48 HIS 0.008 0.001 HIS H 734 Details of bonding type rmsd covalent geometry : bond 0.00404 (28724) covalent geometry : angle 0.62132 (38883) hydrogen bonds : bond 0.04903 ( 1090) hydrogen bonds : angle 5.05440 ( 3108) metal coordination : bond 0.00900 ( 8) metal coordination : angle 3.93893 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 711 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8562 (m) cc_final: 0.8131 (t) REVERT: A 98 GLU cc_start: 0.7029 (tp30) cc_final: 0.6562 (tp30) REVERT: A 159 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: B 140 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8162 (mt) REVERT: B 187 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5964 (tp-100) REVERT: C 42 ASP cc_start: 0.7836 (m-30) cc_final: 0.7581 (m-30) REVERT: C 82 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7413 (ttmm) REVERT: C 171 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: C 183 ARG cc_start: 0.7390 (ttt-90) cc_final: 0.7083 (ttt-90) REVERT: C 572 TYR cc_start: 0.7909 (m-80) cc_final: 0.6520 (m-80) REVERT: C 597 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8094 (mtm-85) REVERT: C 966 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8050 (mtt) REVERT: C 981 ARG cc_start: 0.7905 (tmm-80) cc_final: 0.7468 (ttt90) REVERT: C 1097 THR cc_start: 0.8831 (m) cc_final: 0.8501 (p) REVERT: C 1126 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: D 32 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: D 35 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7166 (m-40) REVERT: D 260 ARG cc_start: 0.8460 (mpt180) cc_final: 0.7373 (mtp180) REVERT: D 264 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7683 (ttm110) REVERT: D 274 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7235 (tt) REVERT: D 287 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7331 (mmp) REVERT: D 360 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 629 LYS cc_start: 0.8895 (tmmt) cc_final: 0.8442 (ttpp) REVERT: D 637 SER cc_start: 0.9115 (t) cc_final: 0.8672 (m) REVERT: D 640 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8956 (mm) REVERT: D 748 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8376 (tmt170) REVERT: D 769 GLU cc_start: 0.7654 (tt0) cc_final: 0.7381 (tt0) REVERT: D 835 THR cc_start: 0.8054 (m) cc_final: 0.7576 (t) REVERT: D 837 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7495 (tt0) REVERT: D 975 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8084 (p0) REVERT: D 1025 THR cc_start: 0.8899 (t) cc_final: 0.8586 (m) REVERT: E 38 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7452 (mttt) REVERT: H 14 ARG cc_start: 0.7918 (mpt180) cc_final: 0.7584 (tpt170) REVERT: H 29 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8206 (mp) REVERT: H 36 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8050 (tt) REVERT: H 86 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: H 87 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: H 91 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8308 (mtm180) REVERT: H 103 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.8013 (ttt180) REVERT: H 195 GLN cc_start: 0.6289 (tm130) cc_final: 0.5038 (mt0) REVERT: H 385 ASN cc_start: 0.7103 (p0) cc_final: 0.6695 (p0) REVERT: H 465 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7142 (t80) REVERT: H 528 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: H 530 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8612 (tt) REVERT: H 543 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8300 (tt) REVERT: H 610 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7140 (t) outliers start: 195 outliers final: 132 residues processed: 836 average time/residue: 0.1837 time to fit residues: 239.5940 Evaluate side-chains 846 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 689 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 748 ARG Chi-restraints excluded: chain D residue 758 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 721 LEU Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 218 optimal weight: 20.0000 chunk 306 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 238 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 187 GLN C 406 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN H 294 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 683 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 = 0.3710 r_free = 0.3710 target = 0.163413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.142036 restraints weight = 38856.961| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.04 r_work: 0.3344 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28732 Z= 0.163 Angle : 0.615 11.016 38895 Z= 0.316 Chirality : 0.045 0.248 4435 Planarity : 0.004 0.054 5058 Dihedral : 6.949 59.741 4036 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 6.66 % Allowed : 25.55 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.42 (0.14), residues: 3611 helix: -0.14 (0.15), residues: 1306 sheet: -0.25 (0.24), residues: 487 loop : -1.77 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.018 0.001 TYR D 650 PHE 0.030 0.001 PHE H 761 TRP 0.011 0.001 TRP H 48 HIS 0.008 0.001 HIS H 734 Details of bonding type rmsd covalent geometry : bond 0.00382 (28724) covalent geometry : angle 0.61172 (38883) hydrogen bonds : bond 0.04752 ( 1090) hydrogen bonds : angle 4.99166 ( 3108) metal coordination : bond 0.00883 ( 8) metal coordination : angle 3.84075 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 725 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8603 (m) cc_final: 0.8152 (t) REVERT: A 84 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8448 (mtmm) REVERT: A 98 GLU cc_start: 0.7007 (tp30) cc_final: 0.6547 (tp30) REVERT: B 140 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8215 (mt) REVERT: C 42 ASP cc_start: 0.7820 (m-30) cc_final: 0.7599 (m-30) REVERT: C 82 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7419 (ttmm) REVERT: C 93 ARG cc_start: 0.7538 (mtp85) cc_final: 0.6882 (mtp85) REVERT: C 171 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 183 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.6716 (mtp-110) REVERT: C 572 TYR cc_start: 0.7910 (m-80) cc_final: 0.6473 (m-80) REVERT: C 597 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8140 (mtm-85) REVERT: C 908 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8623 (tp) REVERT: C 966 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7818 (mtt) REVERT: C 981 ARG cc_start: 0.7864 (tmm-80) cc_final: 0.7429 (ttt90) REVERT: C 1004 LEU cc_start: 0.8799 (mp) cc_final: 0.8496 (mp) REVERT: C 1097 THR cc_start: 0.8827 (m) cc_final: 0.8496 (p) REVERT: C 1126 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: D 32 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: D 35 ASN cc_start: 0.7438 (m-40) cc_final: 0.7182 (m-40) REVERT: D 260 ARG cc_start: 0.8458 (mpt180) cc_final: 0.7342 (mtp180) REVERT: D 264 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7638 (ttm110) REVERT: D 274 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7223 (tt) REVERT: D 287 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7296 (mmp) REVERT: D 360 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 629 LYS cc_start: 0.8818 (tmmt) cc_final: 0.8344 (ttpp) REVERT: D 637 SER cc_start: 0.9067 (t) cc_final: 0.8647 (m) REVERT: D 640 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8913 (mm) REVERT: D 835 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7569 (t) REVERT: D 837 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7463 (tt0) REVERT: D 973 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8173 (tp30) REVERT: D 975 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8056 (p0) REVERT: D 1025 THR cc_start: 0.8914 (t) cc_final: 0.8606 (m) REVERT: E 38 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (mttt) REVERT: H 14 ARG cc_start: 0.7912 (mpt180) cc_final: 0.7561 (tpt170) REVERT: H 29 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8185 (mp) REVERT: H 36 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8052 (tt) REVERT: H 86 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: H 87 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: H 91 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8283 (mtm180) REVERT: H 103 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.8001 (ttt180) REVERT: H 195 GLN cc_start: 0.6264 (tm130) cc_final: 0.5072 (mt0) REVERT: H 300 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7488 (ttp80) REVERT: H 385 ASN cc_start: 0.7196 (p0) cc_final: 0.6807 (p0) REVERT: H 419 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: H 439 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7182 (ttpp) REVERT: H 465 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7145 (t80) REVERT: H 528 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: H 530 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8585 (tt) REVERT: H 543 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8317 (tt) REVERT: H 610 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7149 (t) outliers start: 200 outliers final: 141 residues processed: 853 average time/residue: 0.1873 time to fit residues: 249.3300 Evaluate side-chains 868 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 701 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 419 GLU Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 683 HIS Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 721 LEU Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 355 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 323 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN H 287 ASN H 294 GLN H 454 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 683 HIS H 771 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.161790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.140206 restraints weight = 38737.560| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.07 r_work: 0.3320 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28732 Z= 0.212 Angle : 0.661 11.387 38895 Z= 0.339 Chirality : 0.046 0.228 4435 Planarity : 0.005 0.056 5058 Dihedral : 7.061 59.139 4034 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.31 % Favored : 93.66 % Rotamer: Outliers : 7.23 % Allowed : 25.38 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.45 (0.13), residues: 3611 helix: -0.18 (0.15), residues: 1299 sheet: -0.27 (0.24), residues: 487 loop : -1.76 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 827 TYR 0.020 0.002 TYR D 650 PHE 0.033 0.002 PHE H 761 TRP 0.012 0.001 TRP H 48 HIS 0.009 0.001 HIS H 694 Details of bonding type rmsd covalent geometry : bond 0.00504 (28724) covalent geometry : angle 0.65722 (38883) hydrogen bonds : bond 0.05187 ( 1090) hydrogen bonds : angle 5.10625 ( 3108) metal coordination : bond 0.01065 ( 8) metal coordination : angle 4.15427 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 704 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8614 (m) cc_final: 0.8168 (t) REVERT: A 84 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8463 (mtmm) REVERT: A 98 GLU cc_start: 0.7033 (tp30) cc_final: 0.6584 (tp30) REVERT: A 159 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: B 140 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8207 (mt) REVERT: C 42 ASP cc_start: 0.7792 (m-30) cc_final: 0.7531 (m-30) REVERT: C 82 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7428 (ttmm) REVERT: C 171 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: C 504 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7383 (mtt90) REVERT: C 572 TYR cc_start: 0.7898 (m-80) cc_final: 0.6363 (m-80) REVERT: C 597 ARG cc_start: 0.8475 (ttm110) cc_final: 0.8189 (mtm-85) REVERT: C 607 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.5892 (mtm180) REVERT: C 908 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8614 (tp) REVERT: C 966 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: C 981 ARG cc_start: 0.7907 (tmm-80) cc_final: 0.7480 (ttt90) REVERT: C 1004 LEU cc_start: 0.8787 (mp) cc_final: 0.8469 (mp) REVERT: C 1097 THR cc_start: 0.8854 (m) cc_final: 0.8524 (p) REVERT: C 1126 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: D 32 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: D 158 TYR cc_start: 0.7735 (m-80) cc_final: 0.6516 (t80) REVERT: D 260 ARG cc_start: 0.8504 (mpt180) cc_final: 0.7328 (mtp180) REVERT: D 264 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7686 (ttm110) REVERT: D 274 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7168 (tt) REVERT: D 287 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7332 (mmp) REVERT: D 360 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 437 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8042 (mtt-85) REVERT: D 629 LYS cc_start: 0.8896 (tmmt) cc_final: 0.8405 (ttpp) REVERT: D 637 SER cc_start: 0.9103 (t) cc_final: 0.8670 (m) REVERT: D 640 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8932 (mm) REVERT: D 835 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7642 (t) REVERT: D 975 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8430 (p0) REVERT: E 38 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7516 (mttt) REVERT: H 29 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8152 (mp) REVERT: H 36 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8102 (tt) REVERT: H 86 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: H 87 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7755 (mm-40) REVERT: H 91 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8309 (mtm180) REVERT: H 103 ARG cc_start: 0.8242 (tmm-80) cc_final: 0.8012 (ttt180) REVERT: H 195 GLN cc_start: 0.6526 (tm130) cc_final: 0.5372 (mp10) REVERT: H 300 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: H 385 ASN cc_start: 0.7222 (p0) cc_final: 0.6844 (p0) REVERT: H 419 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: H 439 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7207 (ttpp) REVERT: H 465 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7098 (t80) REVERT: H 528 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: H 530 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8628 (tt) REVERT: H 543 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (tt) REVERT: H 610 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7266 (t) outliers start: 217 outliers final: 160 residues processed: 847 average time/residue: 0.1839 time to fit residues: 241.7078 Evaluate side-chains 883 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 693 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 758 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 419 GLU Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 683 HIS Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 721 LEU Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 65 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 chunk 269 optimal weight: 0.0470 chunk 83 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 114 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN H 12 GLN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN H 454 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 683 HIS H 771 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.162755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.141264 restraints weight = 38884.177| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.06 r_work: 0.3332 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28732 Z= 0.175 Angle : 0.644 11.469 38895 Z= 0.330 Chirality : 0.046 0.352 4435 Planarity : 0.004 0.055 5058 Dihedral : 6.976 57.219 4034 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 6.86 % Allowed : 26.38 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.39 (0.14), residues: 3611 helix: -0.13 (0.15), residues: 1303 sheet: -0.20 (0.24), residues: 482 loop : -1.73 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 539 TYR 0.018 0.001 TYR D 650 PHE 0.032 0.002 PHE H 761 TRP 0.012 0.001 TRP H 48 HIS 0.015 0.001 HIS H 683 Details of bonding type rmsd covalent geometry : bond 0.00414 (28724) covalent geometry : angle 0.63968 (38883) hydrogen bonds : bond 0.04905 ( 1090) hydrogen bonds : angle 5.04110 ( 3108) metal coordination : bond 0.00961 ( 8) metal coordination : angle 4.17678 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 711 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8607 (m) cc_final: 0.8158 (t) REVERT: A 84 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8448 (mtmm) REVERT: A 98 GLU cc_start: 0.6985 (tp30) cc_final: 0.6543 (tp30) REVERT: A 159 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6894 (pt0) REVERT: B 140 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8168 (mt) REVERT: B 227 LEU cc_start: 0.8402 (mt) cc_final: 0.8166 (tt) REVERT: C 42 ASP cc_start: 0.7756 (m-30) cc_final: 0.7499 (m-30) REVERT: C 82 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7419 (ttmm) REVERT: C 504 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7365 (mtt90) REVERT: C 572 TYR cc_start: 0.7940 (m-80) cc_final: 0.6391 (m-80) REVERT: C 597 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8192 (mtm-85) REVERT: C 607 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5929 (mtm180) REVERT: C 908 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8625 (tp) REVERT: C 966 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8134 (mtt) REVERT: C 981 ARG cc_start: 0.7920 (tmm-80) cc_final: 0.7476 (ttt90) REVERT: C 1004 LEU cc_start: 0.8776 (mp) cc_final: 0.8459 (mp) REVERT: C 1097 THR cc_start: 0.8831 (m) cc_final: 0.8500 (p) REVERT: C 1126 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6306 (tm-30) REVERT: D 32 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: D 260 ARG cc_start: 0.8493 (mpt180) cc_final: 0.7314 (mtp180) REVERT: D 264 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7648 (ttm110) REVERT: D 274 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7215 (tt) REVERT: D 287 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7304 (mmp) REVERT: D 360 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 391 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 437 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8041 (mtt-85) REVERT: D 629 LYS cc_start: 0.8826 (tmmt) cc_final: 0.8335 (ttpp) REVERT: D 637 SER cc_start: 0.9075 (t) cc_final: 0.8657 (m) REVERT: D 640 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8923 (mm) REVERT: D 835 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7626 (t) REVERT: D 975 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8425 (p0) REVERT: E 38 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7496 (mttt) REVERT: H 14 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7529 (tpt170) REVERT: H 29 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8131 (mp) REVERT: H 36 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8070 (tt) REVERT: H 86 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: H 87 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7733 (mm-40) REVERT: H 91 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8303 (mtm180) REVERT: H 103 ARG cc_start: 0.8241 (tmm-80) cc_final: 0.8007 (ttt180) REVERT: H 195 GLN cc_start: 0.6547 (tm130) cc_final: 0.5480 (mp10) REVERT: H 300 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7562 (ttp80) REVERT: H 385 ASN cc_start: 0.7239 (p0) cc_final: 0.6867 (p0) REVERT: H 419 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: H 439 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7149 (ttpp) REVERT: H 465 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7153 (t80) REVERT: H 528 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: H 530 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8434 (tt) REVERT: H 543 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (tt) REVERT: H 610 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7234 (t) outliers start: 206 outliers final: 158 residues processed: 843 average time/residue: 0.1862 time to fit residues: 243.6619 Evaluate side-chains 885 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 698 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 758 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 975 ASP Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1019 THR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1163 GLU Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 341 PHE Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 419 GLU Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 683 HIS Chi-restraints excluded: chain H residue 704 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 721 LEU Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 10 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 chunk 321 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 261 optimal weight: 0.0000 chunk 275 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 114 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 GLN H 88 GLN H 287 ASN H 294 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 771 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.165658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.144098 restraints weight = 38829.690| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.06 r_work: 0.3371 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28732 Z= 0.122 Angle : 0.607 11.262 38895 Z= 0.311 Chirality : 0.044 0.377 4435 Planarity : 0.004 0.052 5058 Dihedral : 6.638 56.825 4030 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 5.46 % Allowed : 27.95 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.18 (0.14), residues: 3611 helix: 0.04 (0.15), residues: 1304 sheet: -0.05 (0.24), residues: 479 loop : -1.62 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 539 TYR 0.015 0.001 TYR D 650 PHE 0.030 0.001 PHE H 761 TRP 0.010 0.001 TRP A 199 HIS 0.020 0.001 HIS H 683 Details of bonding type rmsd covalent geometry : bond 0.00277 (28724) covalent geometry : angle 0.60442 (38883) hydrogen bonds : bond 0.04207 ( 1090) hydrogen bonds : angle 4.85399 ( 3108) metal coordination : bond 0.00597 ( 8) metal coordination : angle 3.42864 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 717 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8555 (m) cc_final: 0.8137 (t) REVERT: A 84 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8448 (mtmm) REVERT: A 159 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: B 140 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 42 ASP cc_start: 0.7742 (m-30) cc_final: 0.7489 (m-30) REVERT: C 82 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7500 (ttmm) REVERT: C 536 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7927 (mtmm) REVERT: C 572 TYR cc_start: 0.7973 (m-80) cc_final: 0.6377 (m-80) REVERT: C 597 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8176 (mtm-85) REVERT: C 599 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: C 981 ARG cc_start: 0.7902 (tmm-80) cc_final: 0.7554 (ttt90) REVERT: C 1004 LEU cc_start: 0.8771 (mp) cc_final: 0.8451 (mp) REVERT: C 1097 THR cc_start: 0.8765 (m) cc_final: 0.8466 (p) REVERT: C 1126 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: D 89 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8217 (ptm160) REVERT: D 193 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7117 (mm-30) REVERT: D 260 ARG cc_start: 0.8365 (mpt180) cc_final: 0.7351 (mtp180) REVERT: D 264 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7613 (ttm110) REVERT: D 274 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7251 (tt) REVERT: D 287 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7280 (mmp) REVERT: D 360 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7895 (mt-10) REVERT: D 391 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 437 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8019 (mtt-85) REVERT: D 544 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7848 (pt) REVERT: D 629 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8275 (ttpp) REVERT: D 637 SER cc_start: 0.8981 (t) cc_final: 0.8639 (m) REVERT: D 835 THR cc_start: 0.8040 (m) cc_final: 0.7556 (t) REVERT: D 837 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7431 (tt0) REVERT: E 38 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7441 (tttt) REVERT: H 14 ARG cc_start: 0.7800 (mpt180) cc_final: 0.7540 (tpt-90) REVERT: H 29 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (mp) REVERT: H 36 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8041 (tt) REVERT: H 86 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: H 87 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7706 (mm-40) REVERT: H 91 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (mtm180) REVERT: H 103 ARG cc_start: 0.8235 (tmm-80) cc_final: 0.7999 (ttt180) REVERT: H 195 GLN cc_start: 0.6587 (tm130) cc_final: 0.5616 (mp10) REVERT: H 300 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7579 (ttp80) REVERT: H 385 ASN cc_start: 0.7267 (p0) cc_final: 0.6895 (p0) REVERT: H 419 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: H 465 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7130 (t80) REVERT: H 499 LYS cc_start: 0.7907 (tppt) cc_final: 0.7697 (tppt) REVERT: H 528 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: H 543 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8317 (tt) REVERT: H 582 THR cc_start: 0.0783 (OUTLIER) cc_final: 0.0464 (p) REVERT: H 610 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7128 (t) outliers start: 164 outliers final: 114 residues processed: 822 average time/residue: 0.1849 time to fit residues: 236.3285 Evaluate side-chains 834 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 698 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1163 GLU Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 341 PHE Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 419 GLU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 690 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 269 optimal weight: 0.3980 chunk 208 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 114 HIS C 219 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 988 GLN H 12 GLN H 88 GLN H 287 ASN H 294 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 771 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.163203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.141543 restraints weight = 38682.388| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.08 r_work: 0.3347 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.078 28732 Z= 0.187 Angle : 0.654 11.799 38895 Z= 0.333 Chirality : 0.046 0.218 4435 Planarity : 0.004 0.054 5058 Dihedral : 6.662 57.895 4025 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 5.23 % Allowed : 27.98 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.28 (0.14), residues: 3611 helix: -0.04 (0.15), residues: 1307 sheet: -0.14 (0.24), residues: 482 loop : -1.67 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 93 TYR 0.019 0.002 TYR D 650 PHE 0.028 0.002 PHE H 761 TRP 0.011 0.001 TRP H 48 HIS 0.009 0.001 HIS H 734 Details of bonding type rmsd covalent geometry : bond 0.00445 (28724) covalent geometry : angle 0.65044 (38883) hydrogen bonds : bond 0.04832 ( 1090) hydrogen bonds : angle 4.96371 ( 3108) metal coordination : bond 0.00986 ( 8) metal coordination : angle 4.04014 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 694 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8580 (m) cc_final: 0.8143 (t) REVERT: A 84 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8504 (mtmm) REVERT: A 98 GLU cc_start: 0.7009 (tp30) cc_final: 0.6584 (tp30) REVERT: A 159 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: B 140 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 42 ASP cc_start: 0.7773 (m-30) cc_final: 0.7554 (m-30) REVERT: C 82 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7451 (ttmm) REVERT: C 536 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7928 (mtmm) REVERT: C 572 TYR cc_start: 0.7985 (m-80) cc_final: 0.6431 (m-80) REVERT: C 597 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8181 (mtm-85) REVERT: C 599 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: C 981 ARG cc_start: 0.7942 (tmm-80) cc_final: 0.7476 (ttt90) REVERT: C 1004 LEU cc_start: 0.8803 (mp) cc_final: 0.8466 (mp) REVERT: C 1097 THR cc_start: 0.8819 (m) cc_final: 0.8510 (p) REVERT: C 1126 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: D 158 TYR cc_start: 0.7691 (m-80) cc_final: 0.6505 (t80) REVERT: D 193 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7160 (mm-30) REVERT: D 260 ARG cc_start: 0.8454 (mpt180) cc_final: 0.7375 (mtp180) REVERT: D 264 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7646 (ttm110) REVERT: D 274 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7225 (tt) REVERT: D 287 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7304 (mmp) REVERT: D 360 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 391 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8182 (mt-10) REVERT: D 437 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: D 629 LYS cc_start: 0.8832 (tmmt) cc_final: 0.8348 (ttpp) REVERT: D 637 SER cc_start: 0.9037 (t) cc_final: 0.8685 (m) REVERT: D 835 THR cc_start: 0.8064 (m) cc_final: 0.7614 (t) REVERT: E 38 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7483 (tttt) REVERT: H 14 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7579 (tpt170) REVERT: H 29 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8189 (mp) REVERT: H 36 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8098 (tt) REVERT: H 86 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: H 87 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7748 (mm-40) REVERT: H 91 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8314 (mtm180) REVERT: H 103 ARG cc_start: 0.8274 (tmm-80) cc_final: 0.8039 (ttt180) REVERT: H 195 GLN cc_start: 0.6865 (tm130) cc_final: 0.5875 (mp10) REVERT: H 300 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7515 (ttp80) REVERT: H 385 ASN cc_start: 0.7256 (p0) cc_final: 0.6889 (p0) REVERT: H 419 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: H 465 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7111 (t80) REVERT: H 499 LYS cc_start: 0.7949 (tppt) cc_final: 0.7715 (tppt) REVERT: H 528 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: H 530 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8492 (tt) REVERT: H 582 THR cc_start: 0.0919 (OUTLIER) cc_final: 0.0582 (p) REVERT: H 610 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7229 (t) REVERT: H 683 HIS cc_start: 0.7187 (m-70) cc_final: 0.6944 (t-90) outliers start: 157 outliers final: 118 residues processed: 797 average time/residue: 0.1865 time to fit residues: 230.8779 Evaluate side-chains 826 residues out of total 3145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 687 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 951 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 SER Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1126 GLU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 896 HIS Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1006 TYR Chi-restraints excluded: chain D residue 1023 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1163 GLU Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 205 GLN Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain H residue 419 GLU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 472 VAL Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 528 GLN Chi-restraints excluded: chain H residue 530 LEU Chi-restraints excluded: chain H residue 561 SER Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 581 HIS Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 645 HIS Chi-restraints excluded: chain H residue 669 VAL Chi-restraints excluded: chain H residue 718 ASP Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain H residue 762 VAL Chi-restraints excluded: chain H residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 336 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 232 optimal weight: 0.2980 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN B 114 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 HIS D 585 ASN H 12 GLN H 88 GLN H 287 ASN H 294 GLN ** H 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 771 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.165577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.143895 restraints weight = 38664.019| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.08 r_work: 0.3376 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28732 Z= 0.122 Angle : 0.621 11.909 38895 Z= 0.317 Chirality : 0.044 0.195 4435 Planarity : 0.004 0.052 5058 Dihedral : 6.531 57.513 4025 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.66 % Rotamer: Outliers : 4.93 % Allowed : 28.65 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -1.14 (0.14), residues: 3611 helix: 0.07 (0.15), residues: 1304 sheet: -0.05 (0.24), residues: 479 loop : -1.58 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 93 TYR 0.015 0.001 TYR D 650 PHE 0.029 0.001 PHE H 761 TRP 0.011 0.001 TRP H 48 HIS 0.010 0.001 HIS H 694 Details of bonding type rmsd covalent geometry : bond 0.00278 (28724) covalent geometry : angle 0.61843 (38883) hydrogen bonds : bond 0.04260 ( 1090) hydrogen bonds : angle 4.84909 ( 3108) metal coordination : bond 0.00580 ( 8) metal coordination : angle 3.45931 ( 12) =============================================================================== Job complete usr+sys time: 8123.98 seconds wall clock time: 139 minutes 16.79 seconds (8356.79 seconds total)