Starting phenix.real_space_refine on Sat Aug 8 18:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8syi_40874/08_2026/8syi_40874.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 18179 2.51 5 N 5265 2.21 5 O 5880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29500 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "C" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8382 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 59, 'TRANS': 1001} Chain breaks: 1 Chain: "D" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4961 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 32, 'TRANS': 587} Chain: "Z" Number of atoms: 9357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9357 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 46, 'TRANS': 1174} Chain breaks: 3 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "G" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 745 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12382 SG CYS D 70 48.424 127.240 97.226 1.00112.12 S ATOM 12398 SG CYS D 72 49.973 130.156 95.264 1.00112.11 S ATOM 12507 SG CYS D 85 46.233 129.492 95.178 1.00111.11 S ATOM 12533 SG CYS D 88 48.800 126.998 93.578 1.00113.28 S ATOM 18529 SG CYS Z 221 27.316 71.459 132.195 1.00 49.30 S ATOM 19085 SG CYS Z 295 30.483 72.129 129.972 1.00 35.82 S ATOM 19134 SG CYS Z 302 29.859 73.750 133.373 1.00 39.95 S ATOM 19158 SG CYS Z 305 30.803 70.217 133.314 1.00 49.73 S Time building chain proxies: 6.13, per 1000 atoms: 0.21 Number of scatterers: 29500 At special positions: 0 Unit cell: (139.2, 146.16, 215.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 90 15.00 Mg 1 11.99 O 5880 8.00 N 5265 7.00 C 18179 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 85 " pdb=" ZN Z1401 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 302 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 221 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 305 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 295 " Number of angles added : 12 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6516 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 54 sheets defined 30.5% alpha, 17.6% beta 33 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 4.078A pdb=" N THR A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.817A pdb=" N ASN A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.685A pdb=" N THR B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 206 through 221 removed outlier: 3.619A pdb=" N ALA B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 219 " --> pdb=" O CYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.652A pdb=" N GLU C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 182 through 189 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.594A pdb=" N ILE C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 200 " --> pdb=" O ILE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 4.099A pdb=" N TYR C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 248 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.685A pdb=" N GLY C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.698A pdb=" N ILE C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 341 removed outlier: 4.044A pdb=" N THR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.910A pdb=" N SER C 370 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 388 removed outlier: 3.839A pdb=" N LYS C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 4.008A pdb=" N TYR C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.726A pdb=" N ASP C 475 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 476 " --> pdb=" O GLN C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 527 through 531 removed outlier: 3.640A pdb=" N LEU C 530 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 531 " --> pdb=" O THR C 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 527 through 531' Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 538 through 549 Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.552A pdb=" N ALA C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.517A pdb=" N TYR C 680 " --> pdb=" O GLU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 718 Processing helix chain 'C' and resid 855 through 859 removed outlier: 3.719A pdb=" N GLY C 858 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 859 " --> pdb=" O PRO C 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 855 through 859' Processing helix chain 'C' and resid 865 through 881 removed outlier: 3.719A pdb=" N PHE C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 914 removed outlier: 3.510A pdb=" N LEU C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.516A pdb=" N VAL C 918 " --> pdb=" O GLN C 915 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 919 " --> pdb=" O PRO C 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 915 through 919' Processing helix chain 'C' and resid 955 through 959 Processing helix chain 'C' and resid 978 through 982 removed outlier: 3.785A pdb=" N GLN C 982 " --> pdb=" O LYS C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 998 Processing helix chain 'C' and resid 1001 through 1009 Processing helix chain 'C' and resid 1016 through 1028 removed outlier: 3.565A pdb=" N GLU C1020 " --> pdb=" O GLN C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1049 removed outlier: 3.910A pdb=" N LYS C1041 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 3.705A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.540A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.774A pdb=" N VAL D 97 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.609A pdb=" N GLN D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 200 through 214 removed outlier: 4.018A pdb=" N GLU D 214 " --> pdb=" O GLN D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 270 through 292 removed outlier: 3.560A pdb=" N LEU D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.823A pdb=" N ASN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 339 removed outlier: 4.529A pdb=" N GLY D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.613A pdb=" N LEU D 348 " --> pdb=" O PHE D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.760A pdb=" N ILE D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 412 through 422 removed outlier: 3.844A pdb=" N ASP D 416 " --> pdb=" O PRO D 412 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 459 through 464 Processing helix chain 'D' and resid 479 through 490 Processing helix chain 'D' and resid 491 through 495 removed outlier: 4.063A pdb=" N ASN D 495 " --> pdb=" O ALA D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 521 removed outlier: 3.989A pdb=" N LEU D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.850A pdb=" N ALA D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 608 through 624 Processing helix chain 'Z' and resid 16 through 32 removed outlier: 3.562A pdb=" N GLY Z 32 " --> pdb=" O PHE Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 51 removed outlier: 3.809A pdb=" N VAL Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 3.524A pdb=" N ARG Z 89 " --> pdb=" O ASP Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 121 removed outlier: 3.522A pdb=" N ARG Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP Z 105 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN Z 109 " --> pdb=" O TRP Z 105 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 135 Processing helix chain 'Z' and resid 144 through 149 Processing helix chain 'Z' and resid 175 through 211 removed outlier: 3.740A pdb=" N ILE Z 180 " --> pdb=" O VAL Z 176 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Z 181 " --> pdb=" O THR Z 177 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR Z 197 " --> pdb=" O THR Z 193 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA Z 198 " --> pdb=" O ALA Z 194 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP Z 199 " --> pdb=" O LEU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 246 removed outlier: 3.570A pdb=" N ARG Z 245 " --> pdb=" O PRO Z 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 282 Processing helix chain 'Z' and resid 302 through 307 Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.778A pdb=" N ILE Z 325 " --> pdb=" O ALA Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 337 Processing helix chain 'Z' and resid 764 through 768 removed outlier: 3.880A pdb=" N SER Z 767 " --> pdb=" O GLU Z 764 " (cutoff:3.500A) Processing helix chain 'Z' and resid 807 through 811 removed outlier: 3.512A pdb=" N SER Z 811 " --> pdb=" O SER Z 808 " (cutoff:3.500A) Processing helix chain 'Z' and resid 994 through 1003 Processing helix chain 'Z' and resid 1072 through 1088 removed outlier: 3.780A pdb=" N GLU Z1078 " --> pdb=" O HIS Z1074 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1090 through 1117 removed outlier: 3.825A pdb=" N ALA Z1094 " --> pdb=" O GLU Z1090 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN Z1117 " --> pdb=" O VAL Z1113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1122 through 1131 removed outlier: 4.234A pdb=" N ILE Z1126 " --> pdb=" O SER Z1122 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE Z1129 " --> pdb=" O HIS Z1125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1155 through 1167 Processing helix chain 'Z' and resid 1191 through 1197 removed outlier: 3.550A pdb=" N ALA Z1195 " --> pdb=" O SER Z1191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1200 through 1212 Processing helix chain 'Z' and resid 1222 through 1227 removed outlier: 3.517A pdb=" N ILE Z1226 " --> pdb=" O GLU Z1222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1232 through 1236 removed outlier: 3.852A pdb=" N GLY Z1235 " --> pdb=" O ALA Z1232 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 25 through 44 removed outlier: 3.926A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'G' and resid 33 through 48 Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 129 through 137 removed outlier: 3.647A pdb=" N VAL G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 12 removed outlier: 6.758A pdb=" N ARG A 21 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 10 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 19 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 18 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP A 191 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 174 " --> pdb=" O TRP A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 101 removed outlier: 7.289A pdb=" N GLU A 136 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A 57 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU A 138 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 55 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 140 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.855A pdb=" N VAL A 106 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 12 removed outlier: 6.762A pdb=" N ARG B 21 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER B 10 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 19 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 191 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 174 " --> pdb=" O TRP B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98 removed outlier: 3.607A pdb=" N GLN B 94 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 141 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU B 138 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS B 140 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.582A pdb=" N ALA B 127 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.840A pdb=" N GLY C 104 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 84 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 102 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C 86 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU C 100 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 88 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU C 98 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN C 90 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 96 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AB3, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.782A pdb=" N ASN C 126 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 133 through 140 removed outlier: 4.340A pdb=" N HIS C 148 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB6, first strand: chain 'C' and resid 459 through 461 removed outlier: 4.541A pdb=" N ARG C 454 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 497 through 500 Processing sheet with id=AB8, first strand: chain 'C' and resid 563 through 564 removed outlier: 3.639A pdb=" N GLY C 564 " --> pdb=" O PHE C 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 579 through 580 removed outlier: 6.647A pdb=" N ILE C 579 " --> pdb=" O ILE C 639 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 604 through 608 removed outlier: 6.673A pdb=" N HIS C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 590 " --> pdb=" O HIS C 594 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU C 596 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 926 through 927 removed outlier: 7.326A pdb=" N ILE C 672 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 835 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 674 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 673 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ILE C 852 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 657 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 854 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA C 659 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR C 943 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 686 through 697 removed outlier: 6.419A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR C 809 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 686 through 697 removed outlier: 6.419A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 705 through 706 removed outlier: 3.637A pdb=" N GLU C 705 " --> pdb=" O VAL C 743 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 738 through 740 removed outlier: 7.205A pdb=" N LEU C 774 " --> pdb=" O LEU C 739 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 961 through 963 removed outlier: 6.465A pdb=" N CYS D 372 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 448 " --> pdb=" O CYS D 372 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 374 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.818A pdb=" N GLN C 985 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1068 through 1070 removed outlier: 4.864A pdb=" N VAL C1056 " --> pdb=" O VAL C1070 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 112 removed outlier: 6.884A pdb=" N ASN D 246 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ALA D 109 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N VAL D 244 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.789A pdb=" N TYR D 144 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 185 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.807A pdb=" N VAL D 259 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 533 through 535 Processing sheet with id=AD5, first strand: chain 'D' and resid 563 through 565 Processing sheet with id=AD6, first strand: chain 'D' and resid 576 through 577 removed outlier: 3.632A pdb=" N VAL D 576 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 593 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 227 through 229 Processing sheet with id=AD8, first strand: chain 'Z' and resid 232 through 234 removed outlier: 6.620A pdb=" N MET Z 232 " --> pdb=" O LEU Z 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Z 237 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 255 through 256 removed outlier: 6.686A pdb=" N VAL Z 255 " --> pdb=" O LEU Z 264 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 353 through 358 removed outlier: 6.329A pdb=" N ALA Z 358 " --> pdb=" O ILE Z 424 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE Z 424 " --> pdb=" O ALA Z 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 395 through 396 Processing sheet with id=AE3, first strand: chain 'Z' and resid 441 through 446 removed outlier: 4.323A pdb=" N VAL Z 979 " --> pdb=" O VAL Z 445 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 955 through 957 removed outlier: 3.533A pdb=" N GLY Z 451 " --> pdb=" O VAL Z 972 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 460 through 462 Processing sheet with id=AE6, first strand: chain 'Z' and resid 486 through 489 Processing sheet with id=AE7, first strand: chain 'Z' and resid 509 through 517 removed outlier: 6.712A pdb=" N VAL Z 509 " --> pdb=" O GLN Z 875 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN Z 875 " --> pdb=" O VAL Z 509 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA Z 511 " --> pdb=" O GLN Z 873 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN Z 873 " --> pdb=" O ALA Z 511 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR Z 513 " --> pdb=" O CYS Z 871 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS Z 871 " --> pdb=" O THR Z 513 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU Z 515 " --> pdb=" O ILE Z 869 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Z 867 " --> pdb=" O THR Z 517 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 563 through 566 Processing sheet with id=AE9, first strand: chain 'Z' and resid 603 through 605 removed outlier: 3.585A pdb=" N ILE Z 634 " --> pdb=" O LEU Z 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 623 through 625 removed outlier: 4.328A pdb=" N GLN Z 776 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 638 through 639 Processing sheet with id=AF3, first strand: chain 'Z' and resid 692 through 697 removed outlier: 4.021A pdb=" N ASP Z 692 " --> pdb=" O LEU Z 742 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS Z 694 " --> pdb=" O LEU Z 740 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU Z 740 " --> pdb=" O HIS Z 694 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 903 through 904 removed outlier: 3.535A pdb=" N LEU Z 950 " --> pdb=" O VAL Z 904 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 1031 through 1032 Processing sheet with id=AF6, first strand: chain 'Z' and resid 1152 through 1154 Processing sheet with id=AF7, first strand: chain 'G' and resid 53 through 57 removed outlier: 7.827A pdb=" N ALA G 25 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE G 107 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN G 27 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 60 through 66 Processing sheet with id=AF9, first strand: chain 'G' and resid 109 through 111 959 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7762 1.33 - 1.45: 5394 1.45 - 1.57: 16700 1.57 - 1.69: 179 1.69 - 1.82: 138 Bond restraints: 30173 Sorted by residual: bond pdb=" N GLN Z 917 " pdb=" CA GLN Z 917 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.46e+01 bond pdb=" C3' DC T 4 " pdb=" C2' DC T 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC N 15 " pdb=" C2' DC N 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" CA GLU E 44 " pdb=" C GLU E 44 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.38e-02 5.25e+03 8.79e+00 bond pdb=" C3' DG T 6 " pdb=" C2' DG T 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.65e+00 ... (remaining 30168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 40177 1.83 - 3.66: 944 3.66 - 5.48: 130 5.48 - 7.31: 17 7.31 - 9.14: 7 Bond angle restraints: 41275 Sorted by residual: angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.57e+01 angle pdb=" C ASN Z 680 " pdb=" N ASP Z 681 " pdb=" CA ASP Z 681 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" O4' DA T 16 " pdb=" C4' DA T 16 " pdb=" C3' DA T 16 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.06e+01 angle pdb=" C ALA D 535 " pdb=" N ASN D 536 " pdb=" CA ASN D 536 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N3 DT N 16 " pdb=" C4 DT N 16 " pdb=" O4 DT N 16 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 41270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14652 17.94 - 35.88: 2304 35.88 - 53.82: 915 53.82 - 71.76: 222 71.76 - 89.70: 65 Dihedral angle restraints: 18158 sinusoidal: 8023 harmonic: 10135 Sorted by residual: dihedral pdb=" C4' A R 9 " pdb=" C3' A R 9 " pdb=" C2' A R 9 " pdb=" C1' A R 9 " ideal model delta sinusoidal sigma weight residual 36.34 -38.68 75.02 1 3.10e+00 1.04e-01 7.41e+02 dihedral pdb=" C4' A R 8 " pdb=" C3' A R 8 " pdb=" C2' A R 8 " pdb=" C1' A R 8 " ideal model delta sinusoidal sigma weight residual 36.34 -38.58 74.93 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " ideal model delta sinusoidal sigma weight residual 36.34 -38.21 74.55 1 3.10e+00 1.04e-01 7.33e+02 ... (remaining 18155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3858 0.060 - 0.119: 764 0.119 - 0.179: 61 0.179 - 0.239: 17 0.239 - 0.299: 12 Chirality restraints: 4712 Sorted by residual: chirality pdb=" C3' A R 8 " pdb=" C4' A R 8 " pdb=" O3' A R 8 " pdb=" C2' A R 8 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' C R 11 " pdb=" C4' C R 11 " pdb=" O3' C R 11 " pdb=" C2' C R 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' A R 9 " pdb=" C4' A R 9 " pdb=" O3' A R 9 " pdb=" C2' A R 9 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 4709 not shown) Planarity restraints: 5119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Z1131 " -0.757 9.50e-02 1.11e+02 3.39e-01 7.00e+01 pdb=" NE ARG Z1131 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG Z1131 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Z1131 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Z1131 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG Z1016 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO Z1017 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO Z1017 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO Z1017 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 509 " -0.053 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO C 510 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " -0.043 5.00e-02 4.00e+02 ... (remaining 5116 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 787 2.69 - 3.24: 25911 3.24 - 3.80: 42884 3.80 - 4.35: 56651 4.35 - 4.90: 97265 Nonbonded interactions: 223498 Sorted by model distance: nonbonded pdb=" O ILE D 369 " pdb=" ND1 HIS D 370 " model vdw 2.138 3.120 nonbonded pdb=" OD1 ASP D 468 " pdb="MG MG D1001 " model vdw 2.166 2.170 nonbonded pdb=" O THR Z 630 " pdb=" OG1 THR Z 630 " model vdw 2.188 3.040 nonbonded pdb=" N ASP A 73 " pdb=" OD1 ASP A 73 " model vdw 2.203 3.120 nonbonded pdb=" O3' A R 20 " pdb="MG MG D1001 " model vdw 2.209 2.170 ... (remaining 223493 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' selection = chain 'B' } 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 37.250 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.005 0.096 30181 Z= 0.251 Angle : 0.671 9.139 41287 Z= 0.397 Chirality : 0.050 0.299 4712 Planarity : 0.007 0.339 5119 Dihedral : 20.776 89.702 11642 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.74 % Favored : 91.92 % Rotamer: Outliers : 6.06 % Allowed : 31.55 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3515 helix: 0.88 (0.17), residues: 938 sheet: -0.31 (0.22), residues: 547 loop : -2.26 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 883 TYR 0.021 0.001 TYR Z1083 PHE 0.022 0.002 PHE A 3 TRP 0.010 0.001 TRP C 875 HIS 0.006 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.25 (30173) covalent geometry : angle 0.66788 / 0.40 (41275) hydrogen bonds : bond 0.16702 / 11.02 ( 1047) hydrogen bonds : angle 5.97261 / 4.04 ( 2818) metal coordination : bond 0.00744 / 0.34 ( 8) metal coordination : angle 3.93912 / 2.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 264 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 TYR cc_start: 0.7431 (t80) cc_final: 0.7046 (t80) REVERT: D 47 ARG cc_start: 0.8280 (ttm170) cc_final: 0.8034 (tpp-160) REVERT: Z 295 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8401 (t) REVERT: Z 491 LEU cc_start: 0.8341 (tp) cc_final: 0.7946 (tt) REVERT: Z 643 LYS cc_start: -0.0755 (OUTLIER) cc_final: -0.1200 (ttpp) REVERT: G 54 LEU cc_start: 0.8712 (mp) cc_final: 0.8498 (tt) REVERT: G 78 LYS cc_start: 0.9228 (mppt) cc_final: 0.8740 (mppt) REVERT: G 92 ASP cc_start: 0.8933 (m-30) cc_final: 0.8670 (m-30) outliers start: 181 outliers final: 107 residues processed: 434 average time/residue: 0.6801 time to fit residues: 346.5374 Evaluate side-chains 292 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 183 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1039 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 169 ASN Chi-restraints excluded: chain Z residue 199 ASP Chi-restraints excluded: chain Z residue 219 VAL Chi-restraints excluded: chain Z residue 255 VAL Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 295 CYS Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 347 VAL Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 409 SER Chi-restraints excluded: chain Z residue 438 VAL Chi-restraints excluded: chain Z residue 447 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 620 LYS Chi-restraints excluded: chain Z residue 624 GLU Chi-restraints excluded: chain Z residue 630 THR Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 728 TRP Chi-restraints excluded: chain Z residue 733 ASP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 802 GLU Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1164 THR Chi-restraints excluded: chain Z residue 1234 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 667 ASN ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.061513 restraints weight = 65162.975| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.44 r_work: 0.2644 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30181 Z= 0.155 Angle : 0.724 27.686 41287 Z= 0.360 Chirality : 0.056 1.275 4712 Planarity : 0.005 0.151 5119 Dihedral : 14.910 166.041 5019 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 6.32 % Allowed : 31.15 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.24 (0.14), residues: 3515 helix: 1.32 (0.18), residues: 948 sheet: -0.45 (0.22), residues: 576 loop : -2.14 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG Z 709 TYR 0.012 0.001 TYR G 116 PHE 0.022 0.001 PHE A 3 TRP 0.010 0.001 TRP C 875 HIS 0.007 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30173) covalent geometry : angle 0.72148 / 0.36 (41275) hydrogen bonds : bond 0.04796 / 3.29 ( 1047) hydrogen bonds : angle 4.85768 / 3.28 ( 2818) metal coordination : bond 0.00985 / 0.48 ( 8) metal coordination : angle 3.61306 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 207 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7641 (tpp-160) cc_final: 0.7336 (tpp80) REVERT: A 190 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8242 (pt) REVERT: A 204 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7251 (t) REVERT: B 61 ASN cc_start: 0.8247 (t0) cc_final: 0.7956 (t0) REVERT: B 116 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: B 137 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9175 (mmm) REVERT: C 62 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7489 (mmmm) REVERT: C 302 GLU cc_start: 0.8379 (mp0) cc_final: 0.8037 (mp0) REVERT: C 306 ILE cc_start: 0.9083 (pt) cc_final: 0.8872 (mm) REVERT: C 726 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 1073 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8641 (mpt) REVERT: D 46 TYR cc_start: 0.8142 (t80) cc_final: 0.7224 (t80) REVERT: D 47 ARG cc_start: 0.9017 (ttm170) cc_final: 0.8515 (tpp-160) REVERT: D 174 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8647 (m-10) REVERT: D 216 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (mmtt) REVERT: Z 212 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8759 (pt0) REVERT: Z 295 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7647 (t) REVERT: Z 355 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9005 (mp) REVERT: Z 643 LYS cc_start: 0.4839 (OUTLIER) cc_final: 0.2977 (tmmt) REVERT: Z 683 LEU cc_start: -0.0638 (OUTLIER) cc_final: -0.2506 (pp) REVERT: Z 773 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8601 (mmm160) REVERT: Z 886 GLN cc_start: 0.7641 (tp40) cc_final: 0.6545 (tm-30) REVERT: Z 949 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8346 (pp30) REVERT: Z 1016 ARG cc_start: 0.6873 (tmm-80) cc_final: 0.6561 (tmm-80) REVERT: Z 1033 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7998 (tm130) REVERT: Z 1146 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8911 (pp) REVERT: Z 1170 MET cc_start: 0.8368 (mpm) cc_final: 0.8072 (mpm) REVERT: G 57 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6606 (tm-30) REVERT: G 78 LYS cc_start: 0.8857 (mppt) cc_final: 0.8604 (mppt) REVERT: G 91 ASP cc_start: 0.8173 (m-30) cc_final: 0.7652 (m-30) REVERT: G 93 ASP cc_start: 0.8708 (p0) cc_final: 0.8381 (p0) REVERT: G 113 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8459 (tmmt) REVERT: G 114 ARG cc_start: 0.8427 (mmm160) cc_final: 0.7747 (mmm-85) REVERT: G 124 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.6052 (mmtt) outliers start: 189 outliers final: 86 residues processed: 376 average time/residue: 0.5854 time to fit residues: 263.2545 Evaluate side-chains 289 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 184 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1044 MET Chi-restraints excluded: chain C residue 1073 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 295 CYS Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 347 VAL Chi-restraints excluded: chain Z residue 351 GLU Chi-restraints excluded: chain Z residue 355 LEU Chi-restraints excluded: chain Z residue 438 VAL Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 594 SER Chi-restraints excluded: chain Z residue 624 GLU Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 630 THR Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 733 ASP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 773 ARG Chi-restraints excluded: chain Z residue 802 GLU Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 949 GLN Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1033 GLN Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 288 optimal weight: 50.0000 chunk 155 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 295 optimal weight: 0.0030 chunk 129 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 503 GLN C 667 ASN C 826 HIS ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.059821 restraints weight = 65621.676| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.43 r_work: 0.2611 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30181 Z= 0.189 Angle : 0.679 25.902 41287 Z= 0.344 Chirality : 0.052 1.052 4712 Planarity : 0.005 0.151 5119 Dihedral : 14.618 156.716 4951 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.28 % Favored : 92.43 % Rotamer: Outliers : 6.02 % Allowed : 31.78 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.16 (0.14), residues: 3515 helix: 1.44 (0.18), residues: 955 sheet: -0.50 (0.22), residues: 602 loop : -2.10 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.000 ARG Z 839 TYR 0.013 0.001 TYR Z 50 PHE 0.024 0.001 PHE A 3 TRP 0.032 0.001 TRP Z 728 HIS 0.010 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (30173) covalent geometry : angle 0.67634 / 0.34 (41275) hydrogen bonds : bond 0.05036 / 3.46 ( 1047) hydrogen bonds : angle 4.63882 / 3.15 ( 2818) metal coordination : bond 0.01186 / 0.61 ( 8) metal coordination : angle 3.40056 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 181 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ASN cc_start: 0.8448 (t0) cc_final: 0.8151 (t0) REVERT: B 116 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: C 38 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 302 GLU cc_start: 0.8473 (mp0) cc_final: 0.8072 (mp0) REVERT: C 306 ILE cc_start: 0.9111 (pt) cc_final: 0.8879 (mm) REVERT: C 726 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8406 (pp) REVERT: C 1073 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8662 (mpt) REVERT: D 46 TYR cc_start: 0.8207 (t80) cc_final: 0.7415 (t80) REVERT: D 47 ARG cc_start: 0.9034 (ttm170) cc_final: 0.8583 (tpp-160) REVERT: D 77 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (ptt90) REVERT: D 174 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: D 265 ARG cc_start: 0.8660 (mtm180) cc_final: 0.8451 (mtp180) REVERT: Z 195 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8325 (mt) REVERT: Z 212 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8779 (pt0) REVERT: Z 295 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7702 (t) REVERT: Z 491 LEU cc_start: 0.8182 (tp) cc_final: 0.7840 (tm) REVERT: Z 643 LYS cc_start: 0.4699 (OUTLIER) cc_final: 0.3102 (tmmt) REVERT: Z 677 THR cc_start: 0.2590 (OUTLIER) cc_final: 0.2305 (m) REVERT: Z 683 LEU cc_start: -0.0567 (OUTLIER) cc_final: -0.2525 (pp) REVERT: Z 728 TRP cc_start: 0.6515 (OUTLIER) cc_final: 0.5906 (t-100) REVERT: Z 804 GLU cc_start: 0.4588 (OUTLIER) cc_final: 0.4156 (tt0) REVERT: Z 1146 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8895 (pp) REVERT: Z 1154 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: Z 1170 MET cc_start: 0.8470 (mpm) cc_final: 0.8249 (mpm) REVERT: E 39 GLN cc_start: 0.8546 (tp40) cc_final: 0.8256 (tp40) REVERT: G 113 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8474 (tmmt) REVERT: G 114 ARG cc_start: 0.8416 (mmm160) cc_final: 0.7741 (mtp-110) outliers start: 180 outliers final: 90 residues processed: 342 average time/residue: 0.6041 time to fit residues: 245.9943 Evaluate side-chains 283 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 178 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1073 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 295 CYS Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 347 VAL Chi-restraints excluded: chain Z residue 354 ARG Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 594 SER Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 677 THR Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 728 TRP Chi-restraints excluded: chain Z residue 733 ASP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 802 GLU Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 241 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 275 optimal weight: 0.0570 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 207 GLN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.060326 restraints weight = 65285.654| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.44 r_work: 0.2627 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30181 Z= 0.147 Angle : 0.637 22.334 41287 Z= 0.325 Chirality : 0.051 1.000 4712 Planarity : 0.005 0.130 5119 Dihedral : 14.471 156.767 4937 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.86 % Favored : 92.89 % Rotamer: Outliers : 5.42 % Allowed : 32.22 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.05 (0.14), residues: 3515 helix: 1.54 (0.18), residues: 953 sheet: -0.45 (0.22), residues: 596 loop : -2.03 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 709 TYR 0.011 0.001 TYR Z 50 PHE 0.022 0.001 PHE A 3 TRP 0.019 0.001 TRP Z 728 HIS 0.010 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (30173) covalent geometry : angle 0.63507 / 0.32 (41275) hydrogen bonds : bond 0.04412 / 3.04 ( 1047) hydrogen bonds : angle 4.51387 / 3.07 ( 2818) metal coordination : bond 0.00958 / 0.50 ( 8) metal coordination : angle 3.10663 / 1.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 189 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7710 (OUTLIER) REVERT: A 95 ILE cc_start: 0.7605 (pp) cc_final: 0.7388 (mm) REVERT: A 112 ASP cc_start: 0.8922 (t0) cc_final: 0.8609 (t0) REVERT: A 174 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8080 (ttp-170) REVERT: B 61 ASN cc_start: 0.8533 (t0) cc_final: 0.8228 (t0) REVERT: B 116 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: C 38 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7493 (mm-30) REVERT: C 40 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7665 (p90) REVERT: C 49 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8163 (ttpp) REVERT: C 178 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8403 (mmp80) REVERT: C 253 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8263 (mtm180) REVERT: C 302 GLU cc_start: 0.8467 (mp0) cc_final: 0.8028 (mp0) REVERT: C 306 ILE cc_start: 0.9118 (pt) cc_final: 0.8903 (mm) REVERT: C 309 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 563 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9083 (t) REVERT: C 604 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8707 (mmmm) REVERT: C 775 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8168 (mtp85) REVERT: C 1073 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8617 (mpt) REVERT: D 46 TYR cc_start: 0.8215 (t80) cc_final: 0.7418 (t80) REVERT: D 47 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8534 (tpp-160) REVERT: D 77 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7753 (ptt90) REVERT: D 167 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9206 (mmm) REVERT: D 174 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8649 (m-10) REVERT: D 265 ARG cc_start: 0.8663 (mtm180) cc_final: 0.8408 (mtm180) REVERT: Z 212 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: Z 299 ARG cc_start: 0.8209 (ppt170) cc_final: 0.7206 (ppt170) REVERT: Z 366 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7652 (tm) REVERT: Z 491 LEU cc_start: 0.8081 (tp) cc_final: 0.7728 (tm) REVERT: Z 643 LYS cc_start: 0.4718 (OUTLIER) cc_final: 0.2982 (tmmm) REVERT: Z 669 GLN cc_start: 0.5417 (OUTLIER) cc_final: 0.4852 (mp10) REVERT: Z 677 THR cc_start: 0.2580 (OUTLIER) cc_final: 0.2301 (m) REVERT: Z 683 LEU cc_start: -0.0316 (OUTLIER) cc_final: -0.2366 (pp) REVERT: Z 709 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5391 (tpp80) REVERT: Z 804 GLU cc_start: 0.4582 (OUTLIER) cc_final: 0.4156 (tt0) REVERT: Z 1016 ARG cc_start: 0.6684 (tmm-80) cc_final: 0.6432 (tmm-80) REVERT: Z 1033 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8018 (tm130) REVERT: Z 1146 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8845 (pp) REVERT: G 57 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6802 (tm-30) REVERT: G 77 GLU cc_start: 0.6696 (mp0) cc_final: 0.6144 (mp0) REVERT: G 78 LYS cc_start: 0.9031 (mppt) cc_final: 0.8388 (mppt) REVERT: G 113 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8486 (tmmt) REVERT: G 114 ARG cc_start: 0.8384 (mmm160) cc_final: 0.7701 (mtp-110) outliers start: 162 outliers final: 91 residues processed: 330 average time/residue: 0.6182 time to fit residues: 242.5250 Evaluate side-chains 287 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 173 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1073 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 295 CYS Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 347 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 594 SER Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 677 THR Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 709 ARG Chi-restraints excluded: chain Z residue 733 ASP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1033 GLN Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 274 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 353 optimal weight: 20.0000 chunk 149 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 242 GLN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN Z 389 ASN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 949 GLN G 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.105693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.059454 restraints weight = 65826.645| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.44 r_work: 0.2613 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30181 Z= 0.171 Angle : 0.637 19.100 41287 Z= 0.326 Chirality : 0.049 0.857 4712 Planarity : 0.005 0.158 5119 Dihedral : 14.358 158.032 4924 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.34 % Favored : 92.38 % Rotamer: Outliers : 5.79 % Allowed : 31.78 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.02 (0.14), residues: 3515 helix: 1.58 (0.18), residues: 955 sheet: -0.52 (0.22), residues: 602 loop : -2.00 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG Z 709 TYR 0.012 0.001 TYR Z 50 PHE 0.023 0.001 PHE A 3 TRP 0.035 0.001 TRP Z 728 HIS 0.010 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (30173) covalent geometry : angle 0.63473 / 0.33 (41275) hydrogen bonds : bond 0.04617 / 3.17 ( 1047) hydrogen bonds : angle 4.48286 / 3.05 ( 2818) metal coordination : bond 0.01052 / 0.55 ( 8) metal coordination : angle 2.92464 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 180 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8954 (t0) cc_final: 0.8592 (t0) REVERT: A 204 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7288 (t) REVERT: B 61 ASN cc_start: 0.8612 (t0) cc_final: 0.8304 (t0) REVERT: B 116 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: C 38 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 40 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7809 (p90) REVERT: C 178 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8413 (mmp80) REVERT: C 302 GLU cc_start: 0.8516 (mp0) cc_final: 0.8083 (mp0) REVERT: C 306 ILE cc_start: 0.9137 (pt) cc_final: 0.8924 (mm) REVERT: C 309 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 563 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.9119 (t) REVERT: C 604 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8718 (mmmm) REVERT: C 726 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 775 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8194 (mtp85) REVERT: C 1073 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8640 (mpt) REVERT: D 46 TYR cc_start: 0.8263 (t80) cc_final: 0.7469 (t80) REVERT: D 47 ARG cc_start: 0.9013 (ttm170) cc_final: 0.8539 (tpp-160) REVERT: D 77 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7857 (ptt90) REVERT: D 167 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9216 (mmm) REVERT: D 168 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (pp20) REVERT: D 174 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (m-10) REVERT: D 265 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8381 (mtm180) REVERT: Z 91 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: Z 212 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: Z 249 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7437 (mmt180) REVERT: Z 295 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7892 (t) REVERT: Z 299 ARG cc_start: 0.8226 (ppt170) cc_final: 0.8015 (pmt-80) REVERT: Z 366 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7718 (tm) REVERT: Z 643 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.3049 (tmmm) REVERT: Z 669 GLN cc_start: 0.5453 (OUTLIER) cc_final: 0.4875 (mp10) REVERT: Z 677 THR cc_start: 0.2572 (OUTLIER) cc_final: 0.2294 (m) REVERT: Z 683 LEU cc_start: -0.0392 (OUTLIER) cc_final: -0.2414 (pp) REVERT: Z 709 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5763 (ttp-170) REVERT: Z 804 GLU cc_start: 0.4574 (OUTLIER) cc_final: 0.4136 (tt0) REVERT: Z 1033 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8035 (tm130) REVERT: Z 1141 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: Z 1146 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8823 (pp) REVERT: Z 1154 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: G 42 GLN cc_start: 0.8429 (tp40) cc_final: 0.8136 (tm-30) REVERT: G 92 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8465 (t0) REVERT: G 113 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8457 (tmmt) REVERT: G 114 ARG cc_start: 0.8353 (mmm160) cc_final: 0.7744 (mmm-85) outliers start: 173 outliers final: 101 residues processed: 335 average time/residue: 0.6009 time to fit residues: 239.7215 Evaluate side-chains 302 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 172 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1073 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain Z residue 68 SER Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 295 CYS Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 347 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 594 SER Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 677 THR Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 709 ARG Chi-restraints excluded: chain Z residue 733 ASP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1033 GLN Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1141 ASP Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 159 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 288 optimal weight: 40.0000 chunk 95 optimal weight: 1.9990 chunk 266 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 864 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058960 restraints weight = 65660.137| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.42 r_work: 0.2600 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30181 Z= 0.191 Angle : 0.640 11.101 41287 Z= 0.330 Chirality : 0.047 0.515 4712 Planarity : 0.005 0.137 5119 Dihedral : 14.434 159.364 4924 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.37 % Favored : 92.35 % Rotamer: Outliers : 6.29 % Allowed : 31.31 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.02 (0.14), residues: 3515 helix: 1.58 (0.18), residues: 956 sheet: -0.55 (0.22), residues: 602 loop : -2.00 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Z 709 TYR 0.013 0.001 TYR Z 50 PHE 0.023 0.001 PHE A 3 TRP 0.058 0.001 TRP Z 728 HIS 0.010 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (30173) covalent geometry : angle 0.63791 / 0.33 (41275) hydrogen bonds : bond 0.04894 / 3.36 ( 1047) hydrogen bonds : angle 4.46950 / 3.04 ( 2818) metal coordination : bond 0.01177 / 0.62 ( 8) metal coordination : angle 2.90637 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 179 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: A 112 ASP cc_start: 0.9004 (t0) cc_final: 0.8637 (t0) REVERT: A 150 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mt) REVERT: A 204 SER cc_start: 0.7755 (OUTLIER) cc_final: 0.7372 (t) REVERT: B 61 ASN cc_start: 0.8698 (t0) cc_final: 0.8380 (t0) REVERT: B 116 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: B 138 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: C 38 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 40 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7708 (p90) REVERT: C 163 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: C 306 ILE cc_start: 0.9191 (pt) cc_final: 0.8981 (mm) REVERT: C 309 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 563 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9105 (t) REVERT: C 604 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: C 726 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8362 (pp) REVERT: C 780 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: D 46 TYR cc_start: 0.8313 (t80) cc_final: 0.7745 (t80) REVERT: D 47 ARG cc_start: 0.9021 (ttm170) cc_final: 0.8592 (tpp-160) REVERT: D 77 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7927 (ptt90) REVERT: D 167 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9235 (mmm) REVERT: D 168 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8892 (pp20) REVERT: D 174 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: D 265 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8355 (mtm180) REVERT: Z 212 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8750 (pt0) REVERT: Z 269 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: Z 299 ARG cc_start: 0.8212 (ppt170) cc_final: 0.7972 (ppt170) REVERT: Z 366 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (tm) REVERT: Z 643 LYS cc_start: 0.4312 (OUTLIER) cc_final: 0.2871 (tmmt) REVERT: Z 669 GLN cc_start: 0.5389 (OUTLIER) cc_final: 0.4859 (mp10) REVERT: Z 683 LEU cc_start: -0.0413 (OUTLIER) cc_final: -0.2416 (pp) REVERT: Z 804 GLU cc_start: 0.4714 (OUTLIER) cc_final: 0.4192 (tt0) REVERT: Z 838 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8481 (pt) REVERT: Z 1141 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: Z 1146 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8796 (pp) REVERT: Z 1154 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: G 77 GLU cc_start: 0.6614 (mp0) cc_final: 0.5994 (mp0) REVERT: G 78 LYS cc_start: 0.8983 (mppt) cc_final: 0.8315 (mtpt) REVERT: G 91 ASP cc_start: 0.7880 (m-30) cc_final: 0.7295 (m-30) REVERT: G 92 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8577 (t0) REVERT: G 113 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8462 (tmmt) REVERT: G 114 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7715 (mmm-85) outliers start: 188 outliers final: 107 residues processed: 348 average time/residue: 0.6102 time to fit residues: 253.3523 Evaluate side-chains 313 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 178 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 545 VAL Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 592 ILE Chi-restraints excluded: chain Z residue 594 SER Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 611 ILE Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 692 ASP Chi-restraints excluded: chain Z residue 728 TRP Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 838 ILE Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 922 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1141 ASP Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 295 optimal weight: 0.8980 chunk 291 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 99 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 ASN C 126 ASN D 402 GLN D 510 GLN D 624 HIS ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 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 = 0.3713 r_free = 0.3713 target = 0.106106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059858 restraints weight = 65199.525| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.45 r_work: 0.2636 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30181 Z= 0.124 Angle : 0.616 11.063 41287 Z= 0.317 Chirality : 0.045 0.344 4712 Planarity : 0.004 0.127 5119 Dihedral : 14.353 160.219 4917 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.20 % Rotamer: Outliers : 4.72 % Allowed : 32.99 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.86 (0.14), residues: 3515 helix: 1.71 (0.18), residues: 952 sheet: -0.34 (0.22), residues: 606 loop : -1.92 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG B 152 TYR 0.012 0.001 TYR Z1024 PHE 0.020 0.001 PHE A 3 TRP 0.050 0.001 TRP Z 728 HIS 0.008 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (30173) covalent geometry : angle 0.61473 / 0.32 (41275) hydrogen bonds : bond 0.03921 / 2.71 ( 1047) hydrogen bonds : angle 4.36515 / 2.96 ( 2818) metal coordination : bond 0.00669 / 0.34 ( 8) metal coordination : angle 2.77496 / 1.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 187 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8085 (tpp-160) REVERT: A 85 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8906 (t) REVERT: A 112 ASP cc_start: 0.9009 (t0) cc_final: 0.8632 (t0) REVERT: B 61 ASN cc_start: 0.8698 (t0) cc_final: 0.8372 (t0) REVERT: B 138 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: B 150 ILE cc_start: 0.8541 (tp) cc_final: 0.8167 (tp) REVERT: C 38 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7648 (mm-30) REVERT: C 40 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7254 (p90) REVERT: C 139 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 163 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: C 563 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9088 (t) REVERT: C 604 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8757 (mmmm) REVERT: C 726 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8385 (pp) REVERT: D 46 TYR cc_start: 0.8296 (t80) cc_final: 0.7717 (t80) REVERT: D 47 ARG cc_start: 0.9012 (ttm170) cc_final: 0.8576 (tpp-160) REVERT: D 77 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7800 (ttp-170) REVERT: D 167 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9211 (mmm) REVERT: D 168 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.9014 (pp20) REVERT: D 174 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8584 (m-10) REVERT: D 265 ARG cc_start: 0.8668 (mtm180) cc_final: 0.8364 (mtm180) REVERT: D 411 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8229 (t0) REVERT: Z 91 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: Z 212 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8753 (pt0) REVERT: Z 269 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: Z 299 ARG cc_start: 0.8206 (ppt170) cc_final: 0.7957 (ppt170) REVERT: Z 366 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7811 (tm) REVERT: Z 643 LYS cc_start: 0.4202 (OUTLIER) cc_final: 0.2799 (tmmm) REVERT: Z 669 GLN cc_start: 0.5494 (OUTLIER) cc_final: 0.4931 (mp10) REVERT: Z 683 LEU cc_start: -0.0264 (OUTLIER) cc_final: -0.2239 (pp) REVERT: Z 838 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8475 (pt) REVERT: Z 877 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8482 (pmtt) REVERT: Z 1146 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8801 (pp) REVERT: Z 1154 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: G 92 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8543 (t0) REVERT: G 113 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8476 (tmmt) REVERT: G 114 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7682 (mmm-85) outliers start: 141 outliers final: 82 residues processed: 310 average time/residue: 0.6370 time to fit residues: 233.8453 Evaluate side-chains 279 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 173 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 611 ILE Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 838 ILE Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 325 optimal weight: 0.0970 chunk 254 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 ASN C 126 ASN C 242 GLN D 510 GLN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 915 GLN ** Z 949 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 = 0.3757 r_free = 0.3757 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062109 restraints weight = 65820.887| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.18 r_work: 0.2702 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30181 Z= 0.129 Angle : 0.624 21.534 41287 Z= 0.317 Chirality : 0.045 0.389 4712 Planarity : 0.005 0.176 5119 Dihedral : 14.310 160.758 4909 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.71 % Favored : 93.00 % Rotamer: Outliers : 4.32 % Allowed : 33.56 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.81 (0.14), residues: 3515 helix: 1.75 (0.18), residues: 951 sheet: -0.28 (0.22), residues: 591 loop : -1.88 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 178 TYR 0.012 0.001 TYR Z1024 PHE 0.020 0.001 PHE A 3 TRP 0.036 0.001 TRP Z 728 HIS 0.009 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (30173) covalent geometry : angle 0.62249 / 0.32 (41275) hydrogen bonds : bond 0.03889 / 2.68 ( 1047) hydrogen bonds : angle 4.30301 / 2.92 ( 2818) metal coordination : bond 0.00703 / 0.36 ( 8) metal coordination : angle 2.63957 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 181 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.9017 (t0) cc_final: 0.8667 (t0) REVERT: A 204 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7643 (t) REVERT: B 61 ASN cc_start: 0.8811 (t0) cc_final: 0.8531 (t0) REVERT: B 138 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: B 150 ILE cc_start: 0.8696 (tp) cc_final: 0.8315 (tp) REVERT: C 38 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7786 (mm-30) REVERT: C 40 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7044 (p90) REVERT: C 163 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: C 178 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8179 (mmm-85) REVERT: C 563 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9144 (t) REVERT: C 604 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8910 (mmmm) REVERT: C 726 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8615 (pp) REVERT: D 46 TYR cc_start: 0.8377 (t80) cc_final: 0.7860 (t80) REVERT: D 47 ARG cc_start: 0.8996 (ttm170) cc_final: 0.8595 (tpp-160) REVERT: D 77 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7873 (ttp-170) REVERT: D 167 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9192 (mmm) REVERT: D 168 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9022 (pp20) REVERT: D 174 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (m-10) REVERT: D 265 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8362 (mtm180) REVERT: Z 91 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: Z 212 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8790 (pt0) REVERT: Z 269 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: Z 299 ARG cc_start: 0.8226 (ppt170) cc_final: 0.7902 (ppt90) REVERT: Z 366 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7772 (tm) REVERT: Z 525 MET cc_start: 0.5721 (pmm) cc_final: 0.4387 (ppp) REVERT: Z 643 LYS cc_start: 0.3725 (OUTLIER) cc_final: 0.2286 (tmmm) REVERT: Z 669 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4577 (mp10) REVERT: Z 683 LEU cc_start: -0.0851 (OUTLIER) cc_final: -0.2717 (pp) REVERT: Z 804 GLU cc_start: 0.4583 (OUTLIER) cc_final: 0.4126 (tt0) REVERT: Z 838 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (pt) REVERT: Z 1146 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8749 (pp) REVERT: Z 1154 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: Z 1170 MET cc_start: 0.8164 (mpm) cc_final: 0.7941 (mpm) REVERT: G 77 GLU cc_start: 0.6711 (mp0) cc_final: 0.6285 (mp0) REVERT: G 78 LYS cc_start: 0.9055 (mppt) cc_final: 0.8506 (mttt) REVERT: G 92 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (t70) REVERT: G 114 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7681 (mmm-85) outliers start: 129 outliers final: 89 residues processed: 294 average time/residue: 0.6403 time to fit residues: 223.3940 Evaluate side-chains 285 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 173 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1044 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 611 ILE Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 838 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 308 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 134 optimal weight: 0.0170 chunk 35 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN D 510 GLN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.058584 restraints weight = 66480.921| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.14 r_work: 0.2627 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 30181 Z= 0.349 Angle : 0.741 16.448 41287 Z= 0.381 Chirality : 0.050 0.381 4712 Planarity : 0.005 0.155 5119 Dihedral : 14.485 161.484 4908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 4.85 % Allowed : 33.02 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.08 (0.14), residues: 3515 helix: 1.44 (0.18), residues: 957 sheet: -0.55 (0.22), residues: 584 loop : -1.98 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 178 TYR 0.018 0.002 TYR Z 50 PHE 0.025 0.002 PHE A 3 TRP 0.030 0.002 TRP Z 728 HIS 0.016 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.35 (30173) covalent geometry : angle 0.73876 / 0.38 (41275) hydrogen bonds : bond 0.06330 / 4.33 ( 1047) hydrogen bonds : angle 4.58421 / 3.13 ( 2818) metal coordination : bond 0.01829 / 0.98 ( 8) metal coordination : angle 3.24069 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 164 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: A 204 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8066 (t) REVERT: B 61 ASN cc_start: 0.8848 (t0) cc_final: 0.8583 (t0) REVERT: B 150 ILE cc_start: 0.8822 (tp) cc_final: 0.8459 (tp) REVERT: C 38 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 40 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7328 (p90) REVERT: C 49 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8692 (tppp) REVERT: C 139 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 163 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: C 178 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8349 (mmp80) REVERT: C 274 ASP cc_start: 0.8950 (p0) cc_final: 0.8734 (p0) REVERT: C 563 VAL cc_start: 0.9467 (OUTLIER) cc_final: 0.9238 (t) REVERT: C 604 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9131 (mmmm) REVERT: D 46 TYR cc_start: 0.8515 (t80) cc_final: 0.8057 (t80) REVERT: D 47 ARG cc_start: 0.9011 (ttm170) cc_final: 0.8604 (tpp-160) REVERT: D 168 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8918 (pp20) REVERT: D 174 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (m-10) REVERT: D 265 ARG cc_start: 0.8676 (mtm180) cc_final: 0.8448 (mtm180) REVERT: Z 91 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: Z 164 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8566 (mp) REVERT: Z 212 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: Z 269 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: Z 366 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7893 (tm) REVERT: Z 643 LYS cc_start: 0.3764 (OUTLIER) cc_final: 0.2346 (tmmm) REVERT: Z 669 GLN cc_start: 0.5036 (OUTLIER) cc_final: 0.4421 (pm20) REVERT: Z 683 LEU cc_start: -0.1077 (OUTLIER) cc_final: -0.2919 (pp) REVERT: Z 804 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.4188 (tt0) REVERT: Z 1146 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8703 (pp) REVERT: Z 1154 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: Z 1170 MET cc_start: 0.8298 (mpm) cc_final: 0.8090 (mpm) REVERT: G 47 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7462 (mm) REVERT: G 92 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8738 (t0) outliers start: 145 outliers final: 95 residues processed: 291 average time/residue: 0.6434 time to fit residues: 222.3401 Evaluate side-chains 286 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 169 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 351 GLU Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 611 ILE Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 651 GLU Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 346 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 273 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 310 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 510 GLN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060558 restraints weight = 65359.735| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.11 r_work: 0.2683 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30181 Z= 0.130 Angle : 0.650 13.752 41287 Z= 0.335 Chirality : 0.045 0.315 4712 Planarity : 0.004 0.058 5119 Dihedral : 14.417 160.989 4908 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.49 % Favored : 93.23 % Rotamer: Outliers : 3.65 % Allowed : 34.46 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.87 (0.14), residues: 3515 helix: 1.68 (0.18), residues: 954 sheet: -0.28 (0.22), residues: 567 loop : -1.92 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 178 TYR 0.011 0.001 TYR Z 50 PHE 0.020 0.001 PHE A 3 TRP 0.029 0.001 TRP Z 728 HIS 0.008 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (30173) covalent geometry : angle 0.64718 / 0.33 (41275) hydrogen bonds : bond 0.04483 / 3.08 ( 1047) hydrogen bonds : angle 4.36918 / 2.97 ( 2818) metal coordination : bond 0.00776 / 0.39 ( 8) metal coordination : angle 3.28539 / 1.79 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 176 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.9010 (t0) cc_final: 0.8696 (t0) REVERT: A 204 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7939 (t) REVERT: B 61 ASN cc_start: 0.8884 (t0) cc_final: 0.8640 (t0) REVERT: B 110 ASP cc_start: 0.9023 (m-30) cc_final: 0.8501 (m-30) REVERT: B 150 ILE cc_start: 0.8793 (tp) cc_final: 0.8408 (tp) REVERT: C 38 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 40 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.6987 (p90) REVERT: C 139 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 163 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: C 178 ARG cc_start: 0.8714 (mmm160) cc_final: 0.8323 (mmp80) REVERT: C 563 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9161 (t) REVERT: C 604 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8936 (mmmm) REVERT: D 46 TYR cc_start: 0.8474 (t80) cc_final: 0.7901 (t80) REVERT: D 47 ARG cc_start: 0.9014 (ttm170) cc_final: 0.8630 (tpp-160) REVERT: D 77 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7942 (ttp80) REVERT: D 168 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.9013 (pp20) REVERT: D 174 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8377 (m-10) REVERT: D 265 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8353 (mtm180) REVERT: D 411 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8434 (t0) REVERT: Z 212 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8841 (pt0) REVERT: Z 269 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: Z 299 ARG cc_start: 0.8267 (ppt170) cc_final: 0.7985 (ppt90) REVERT: Z 366 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7906 (tm) REVERT: Z 525 MET cc_start: 0.5614 (pmm) cc_final: 0.4233 (ppp) REVERT: Z 643 LYS cc_start: 0.3567 (OUTLIER) cc_final: 0.2222 (tmmm) REVERT: Z 669 GLN cc_start: 0.5080 (OUTLIER) cc_final: 0.4436 (pm20) REVERT: Z 683 LEU cc_start: -0.0999 (OUTLIER) cc_final: -0.2831 (pp) REVERT: Z 804 GLU cc_start: 0.4595 (OUTLIER) cc_final: 0.4127 (tt0) REVERT: Z 1146 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8690 (pp) REVERT: Z 1154 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: Z 1170 MET cc_start: 0.8310 (mpm) cc_final: 0.8096 (mpm) REVERT: G 52 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: G 77 GLU cc_start: 0.6790 (mp0) cc_final: 0.6226 (mp0) REVERT: G 78 LYS cc_start: 0.9228 (mppt) cc_final: 0.8566 (mttt) REVERT: G 92 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8764 (t70) outliers start: 109 outliers final: 79 residues processed: 272 average time/residue: 0.6465 time to fit residues: 207.8558 Evaluate side-chains 270 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 172 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 212 GLN Chi-restraints excluded: chain Z residue 260 THR Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 301 VAL Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain Z residue 548 THR Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 611 ILE Chi-restraints excluded: chain Z residue 625 VAL Chi-restraints excluded: chain Z residue 634 ILE Chi-restraints excluded: chain Z residue 643 LYS Chi-restraints excluded: chain Z residue 669 GLN Chi-restraints excluded: chain Z residue 673 ILE Chi-restraints excluded: chain Z residue 674 VAL Chi-restraints excluded: chain Z residue 683 LEU Chi-restraints excluded: chain Z residue 685 GLU Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 769 SER Chi-restraints excluded: chain Z residue 796 ARG Chi-restraints excluded: chain Z residue 804 GLU Chi-restraints excluded: chain Z residue 877 LYS Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 972 VAL Chi-restraints excluded: chain Z residue 992 ILE Chi-restraints excluded: chain Z residue 1013 LEU Chi-restraints excluded: chain Z residue 1025 SER Chi-restraints excluded: chain Z residue 1031 ASP Chi-restraints excluded: chain Z residue 1052 LEU Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1137 VAL Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1154 GLU Chi-restraints excluded: chain Z residue 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 281 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 228 optimal weight: 0.0470 chunk 139 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 GLN D 510 GLN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060484 restraints weight = 66132.141| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.15 r_work: 0.2692 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30181 Z= 0.144 Angle : 0.635 12.922 41287 Z= 0.328 Chirality : 0.045 0.310 4712 Planarity : 0.004 0.060 5119 Dihedral : 14.376 161.250 4907 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.69 % Rotamer: Outliers : 3.75 % Allowed : 34.36 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.84 (0.14), residues: 3515 helix: 1.70 (0.18), residues: 955 sheet: -0.23 (0.23), residues: 552 loop : -1.89 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 178 TYR 0.011 0.001 TYR Z 50 PHE 0.020 0.001 PHE A 3 TRP 0.028 0.001 TRP Z 728 HIS 0.009 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (30173) covalent geometry : angle 0.63335 / 0.33 (41275) hydrogen bonds : bond 0.04376 / 3.01 ( 1047) hydrogen bonds : angle 4.32828 / 2.95 ( 2818) metal coordination : bond 0.00867 / 0.45 ( 8) metal coordination : angle 3.07986 / 1.69 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10883.65 seconds wall clock time: 185 minutes 49.62 seconds (11149.62 seconds total)