Starting phenix.real_space_refine on Sun Jul 5 18:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syi_40874/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.cif" model { file = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_2026/8syi_40874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syi_40874/07_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-dev-6108/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: {'RNA': 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: 5.93, per 1000 atoms: 0.20 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 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: 3.05 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: 7.34 Time building geometry restraints manager: 3.09 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: 40237 1.83 - 3.66: 899 3.66 - 5.48: 115 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: 14691 17.94 - 35.88: 2293 35.88 - 53.82: 906 53.82 - 71.76: 207 71.76 - 89.70: 61 Dihedral angle restraints: 18158 sinusoidal: 8023 harmonic: 10135 Sorted by residual: dihedral pdb=" CA ILE D 120 " pdb=" C ILE D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLU B 63 " pdb=" C GLU B 63 " pdb=" N PHE B 64 " pdb=" CA PHE B 64 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA SER A 187 " pdb=" C SER A 187 " pdb=" N THR A 188 " pdb=" CA THR A 188 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 18155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3627 0.051 - 0.102: 860 0.102 - 0.153: 220 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 4712 Sorted by residual: chirality pdb=" CA PRO Z1017 " pdb=" N PRO Z1017 " pdb=" C PRO Z1017 " pdb=" CB PRO Z1017 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN Z 917 " pdb=" N GLN Z 917 " pdb=" C GLN Z 917 " pdb=" CB GLN Z 917 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ARG Z1131 " pdb=" N ARG Z1131 " pdb=" C ARG Z1131 " pdb=" CB ARG Z1131 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 31.300 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- 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= 0.250 Angle : 0.658 9.139 41287 Z= 0.393 Chirality : 0.046 0.255 4712 Planarity : 0.007 0.339 5119 Dihedral : 20.555 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 0.00459 / 0.25 (30173) covalent geometry : angle 0.65426 / 0.39 (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 : 0.819 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: 0.6362 time to fit residues: 324.5131 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 : 0.669 ------------------------------------------------------------------------------- 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** E 39 GLN G 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061412 restraints weight = 65454.865| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.45 r_work: 0.2642 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30181 Z= 0.144 Angle : 0.623 11.620 41287 Z= 0.331 Chirality : 0.044 0.297 4712 Planarity : 0.005 0.149 5119 Dihedral : 14.409 87.685 5019 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.71 % Favored : 92.97 % Rotamer: Outliers : 6.22 % Allowed : 31.35 % 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: -1.24 (0.14), residues: 3515 helix: 1.34 (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 0.026 0.001 ARG Z 709 TYR 0.013 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 0.00325 / 0.14 (30173) covalent geometry : angle 0.62016 / 0.33 (41275) hydrogen bonds : bond 0.04855 / 3.33 ( 1047) hydrogen bonds : angle 4.86912 / 3.29 ( 2818) metal coordination : bond 0.00954 / 0.47 ( 8) metal coordination : angle 3.71019 / 2.01 ( 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 393 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 207 time to evaluate : 0.738 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: A 29 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7125 (tpp80) REVERT: A 204 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.7251 (t) REVERT: B 61 ASN cc_start: 0.8241 (t0) cc_final: 0.7974 (t0) REVERT: B 116 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: B 137 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9177 (mmm) REVERT: C 62 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7481 (mmmm) REVERT: C 302 GLU cc_start: 0.8367 (mp0) cc_final: 0.8035 (mp0) REVERT: C 306 ILE cc_start: 0.9080 (pt) cc_final: 0.8867 (mm) REVERT: C 726 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8473 (pp) REVERT: C 1073 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8643 (mpt) REVERT: D 46 TYR cc_start: 0.8140 (t80) cc_final: 0.7222 (t80) REVERT: D 47 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8506 (tpp-160) REVERT: D 174 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8643 (m-10) REVERT: D 216 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7821 (mmtt) REVERT: Z 212 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8773 (pt0) REVERT: Z 295 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7636 (t) REVERT: Z 355 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8984 (mp) REVERT: Z 643 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.3468 (ttpp) REVERT: Z 683 LEU cc_start: -0.0605 (OUTLIER) cc_final: -0.2488 (pp) REVERT: Z 773 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (mmm160) REVERT: Z 886 GLN cc_start: 0.7643 (tp40) cc_final: 0.6547 (tm-30) REVERT: Z 949 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8343 (pp30) REVERT: Z 1016 ARG cc_start: 0.6865 (tmm-80) cc_final: 0.6539 (tmm-80) REVERT: Z 1033 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8002 (tm130) REVERT: Z 1146 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8932 (pp) REVERT: Z 1170 MET cc_start: 0.8386 (mpm) cc_final: 0.8105 (mpm) REVERT: G 57 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6594 (tm-30) REVERT: G 78 LYS cc_start: 0.8854 (mppt) cc_final: 0.8602 (mppt) REVERT: G 91 ASP cc_start: 0.8202 (m-30) cc_final: 0.7886 (m-30) REVERT: G 93 ASP cc_start: 0.8706 (p0) cc_final: 0.8320 (p0) REVERT: G 113 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8461 (tmmt) REVERT: G 114 ARG cc_start: 0.8419 (mmm160) cc_final: 0.7761 (mmm-85) REVERT: G 124 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.6043 (mmtt) outliers start: 186 outliers final: 89 residues processed: 373 average time/residue: 0.5752 time to fit residues: 256.1591 Evaluate side-chains 293 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 186 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 B residue 203 LEU 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 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 264 LEU Chi-restraints excluded: chain C residue 321 LEU 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 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 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 255 VAL 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 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: 30.0000 chunk 129 optimal weight: 7.9990 chunk 353 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.105728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059375 restraints weight = 65805.510| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.46 r_work: 0.2608 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30181 Z= 0.193 Angle : 0.617 13.401 41287 Z= 0.328 Chirality : 0.044 0.305 4712 Planarity : 0.005 0.154 5119 Dihedral : 14.167 85.651 4957 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.31 % Favored : 92.40 % Rotamer: Outliers : 6.22 % Allowed : 31.62 % Favored : 62.16 % 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: -1.17 (0.14), residues: 3515 helix: 1.43 (0.18), residues: 955 sheet: -0.51 (0.22), residues: 602 loop : -2.11 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG Z 839 TYR 0.013 0.001 TYR Z 50 PHE 0.024 0.001 PHE A 3 TRP 0.027 0.001 TRP Z 728 HIS 0.011 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (30173) covalent geometry : angle 0.61422 / 0.33 (41275) hydrogen bonds : bond 0.05160 / 3.54 ( 1047) hydrogen bonds : angle 4.64892 / 3.16 ( 2818) metal coordination : bond 0.01211 / 0.62 ( 8) metal coordination : angle 3.46299 / 1.88 ( 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 367 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 181 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ASN cc_start: 0.8466 (t0) cc_final: 0.8167 (t0) REVERT: B 116 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: C 38 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 302 GLU cc_start: 0.8503 (mp0) cc_final: 0.8116 (mp0) REVERT: C 306 ILE cc_start: 0.9134 (pt) cc_final: 0.8897 (mm) REVERT: C 394 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8891 (mt) REVERT: C 649 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: C 726 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 1073 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8680 (mpt) REVERT: D 46 TYR cc_start: 0.8229 (t80) cc_final: 0.7445 (t80) REVERT: D 47 ARG cc_start: 0.9028 (ttm170) cc_final: 0.8568 (tpp-160) REVERT: D 174 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: Z 195 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8378 (mt) REVERT: Z 212 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8798 (pt0) REVERT: Z 295 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7742 (t) REVERT: Z 491 LEU cc_start: 0.8196 (tp) cc_final: 0.7834 (tm) REVERT: Z 643 LYS cc_start: 0.4888 (OUTLIER) cc_final: 0.3366 (tmmt) REVERT: Z 677 THR cc_start: 0.2625 (OUTLIER) cc_final: 0.2348 (m) REVERT: Z 683 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.2295 (pp) REVERT: Z 728 TRP cc_start: 0.6558 (OUTLIER) cc_final: 0.5909 (t-100) REVERT: Z 804 GLU cc_start: 0.4680 (OUTLIER) cc_final: 0.4274 (tt0) REVERT: Z 949 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8461 (pp30) REVERT: Z 1146 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8882 (pp) REVERT: Z 1154 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: Z 1170 MET cc_start: 0.8472 (mpm) cc_final: 0.8244 (mpm) REVERT: G 113 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8460 (tmmt) REVERT: G 114 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7799 (mtp-110) outliers start: 186 outliers final: 92 residues processed: 348 average time/residue: 0.6318 time to fit residues: 261.5350 Evaluate side-chains 284 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 175 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 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 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 518 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 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 GLU 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 88 CYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 291 ILE 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 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 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 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 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 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: 2.9990 chunk 153 optimal weight: 0.4980 chunk 275 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN C 207 GLN C 242 GLN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 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 = 0.3717 r_free = 0.3717 target = 0.106247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.060083 restraints weight = 65301.533| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.43 r_work: 0.2627 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30181 Z= 0.142 Angle : 0.590 10.075 41287 Z= 0.312 Chirality : 0.043 0.294 4712 Planarity : 0.005 0.130 5119 Dihedral : 13.985 85.791 4937 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 5.49 % Allowed : 32.52 % Favored : 61.99 % 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: -1.06 (0.14), residues: 3515 helix: 1.54 (0.18), residues: 954 sheet: -0.47 (0.22), residues: 596 loop : -2.04 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Z 354 TYR 0.011 0.001 TYR Z 50 PHE 0.022 0.001 PHE A 3 TRP 0.018 0.001 TRP Z 728 HIS 0.009 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (30173) covalent geometry : angle 0.58773 / 0.31 (41275) hydrogen bonds : bond 0.04442 / 3.06 ( 1047) hydrogen bonds : angle 4.53982 / 3.08 ( 2818) metal coordination : bond 0.00940 / 0.48 ( 8) metal coordination : angle 3.18545 / 1.75 ( 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 354 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 190 time to evaluate : 1.143 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: A 73 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7705 (p0) REVERT: A 112 ASP cc_start: 0.8929 (t0) cc_final: 0.8620 (t0) REVERT: A 174 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8124 (ttp-170) REVERT: B 61 ASN cc_start: 0.8538 (t0) cc_final: 0.8223 (t0) REVERT: B 116 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: C 38 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 178 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8299 (mmp80) REVERT: C 253 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8285 (mtm180) REVERT: C 302 GLU cc_start: 0.8497 (mp0) cc_final: 0.8069 (mp0) REVERT: C 306 ILE cc_start: 0.9128 (pt) cc_final: 0.8912 (mm) REVERT: C 309 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 394 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8859 (mt) REVERT: C 563 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9099 (t) REVERT: C 604 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: C 649 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: C 775 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8186 (mtp85) REVERT: C 780 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: C 1073 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8627 (mpt) REVERT: D 46 TYR cc_start: 0.8227 (t80) cc_final: 0.7434 (t80) REVERT: D 47 ARG cc_start: 0.9028 (ttm170) cc_final: 0.8557 (tpp-160) REVERT: D 167 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9197 (mmm) REVERT: D 174 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8643 (m-10) REVERT: Z 195 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (mt) REVERT: Z 212 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: Z 299 ARG cc_start: 0.8214 (ppt170) cc_final: 0.7213 (ppt170) REVERT: Z 366 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7610 (tm) REVERT: Z 491 LEU cc_start: 0.8094 (tp) cc_final: 0.7740 (tm) REVERT: Z 643 LYS cc_start: 0.4789 (OUTLIER) cc_final: 0.3079 (tmmm) REVERT: Z 669 GLN cc_start: 0.5463 (OUTLIER) cc_final: 0.4900 (mp10) REVERT: Z 677 THR cc_start: 0.2581 (OUTLIER) cc_final: 0.2303 (m) REVERT: Z 683 LEU cc_start: -0.0251 (OUTLIER) cc_final: -0.2318 (pp) REVERT: Z 709 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5426 (tpp80) REVERT: Z 804 GLU cc_start: 0.4567 (OUTLIER) cc_final: 0.4152 (tt0) REVERT: Z 1016 ARG cc_start: 0.6679 (tmm-80) cc_final: 0.6426 (tmm-80) REVERT: Z 1033 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8023 (tm130) REVERT: Z 1141 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: Z 1146 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8834 (pp) REVERT: G 42 GLN cc_start: 0.8414 (tp40) cc_final: 0.8111 (tm-30) REVERT: G 57 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6810 (tm-30) REVERT: G 77 GLU cc_start: 0.6709 (mp0) cc_final: 0.6234 (mp0) REVERT: G 78 LYS cc_start: 0.9045 (mppt) cc_final: 0.8422 (mppt) REVERT: G 113 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8453 (tmmt) REVERT: G 114 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7727 (mtp-110) outliers start: 164 outliers final: 90 residues processed: 334 average time/residue: 0.6262 time to fit residues: 248.7479 Evaluate side-chains 296 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 180 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 ILE 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 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 200 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 LEU 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 344 ASP 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 394 LEU 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 597 VAL 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 649 GLU Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 780 GLU 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 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 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 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 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 802 GLU 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 1179 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 66 ASP 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: 0.5980 chunk 75 optimal weight: 5.9990 chunk 274 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 208 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN ** 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** G 122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.058605 restraints weight = 66053.625| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.44 r_work: 0.2594 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30181 Z= 0.211 Angle : 0.615 15.834 41287 Z= 0.325 Chirality : 0.045 0.335 4712 Planarity : 0.005 0.160 5119 Dihedral : 13.913 84.653 4927 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.65 % Favored : 92.06 % Rotamer: Outliers : 6.49 % Allowed : 31.15 % 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: -1.09 (0.14), residues: 3515 helix: 1.51 (0.18), residues: 956 sheet: -0.58 (0.22), residues: 602 loop : -2.03 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG Z 709 TYR 0.014 0.001 TYR Z 50 PHE 0.024 0.001 PHE A 3 TRP 0.044 0.001 TRP Z 728 HIS 0.011 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (30173) covalent geometry : angle 0.61255 / 0.32 (41275) hydrogen bonds : bond 0.05105 / 3.51 ( 1047) hydrogen bonds : angle 4.55470 / 3.10 ( 2818) metal coordination : bond 0.01260 / 0.67 ( 8) metal coordination : angle 3.10529 / 1.69 ( 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 372 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 178 time to evaluate : 1.225 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: 0.8969 (t0) cc_final: 0.8624 (t0) REVERT: A 204 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7364 (t) REVERT: B 61 ASN cc_start: 0.8620 (t0) cc_final: 0.8289 (t0) REVERT: B 116 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: B 138 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: C 38 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7640 (mm-30) REVERT: C 40 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7775 (p90) REVERT: C 178 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8437 (mmp80) REVERT: C 253 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8287 (mtm180) REVERT: C 302 GLU cc_start: 0.8525 (mp0) cc_final: 0.8110 (mp0) REVERT: C 306 ILE cc_start: 0.9164 (pt) cc_final: 0.8936 (mm) REVERT: C 563 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9153 (t) REVERT: C 604 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: C 649 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: C 726 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 780 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: D 46 TYR cc_start: 0.8277 (t80) cc_final: 0.7494 (t80) REVERT: D 47 ARG cc_start: 0.9015 (ttm170) cc_final: 0.8544 (tpp-160) REVERT: D 167 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9214 (mmm) REVERT: D 174 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8628 (m-10) REVERT: Z 212 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8763 (pt0) REVERT: Z 299 ARG cc_start: 0.8239 (ppt170) cc_final: 0.7992 (ppt170) REVERT: Z 366 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7698 (tm) REVERT: Z 643 LYS cc_start: 0.4716 (OUTLIER) cc_final: 0.3094 (tmmm) REVERT: Z 669 GLN cc_start: 0.5388 (OUTLIER) cc_final: 0.4866 (mp10) REVERT: Z 677 THR cc_start: 0.2574 (OUTLIER) cc_final: 0.2295 (m) REVERT: Z 683 LEU cc_start: -0.0358 (OUTLIER) cc_final: -0.2381 (pp) REVERT: Z 709 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5728 (ttp-170) REVERT: Z 804 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4220 (tt0) REVERT: Z 1033 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8042 (tm130) REVERT: Z 1141 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: Z 1146 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8819 (pp) REVERT: Z 1154 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: G 113 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8412 (tmmt) REVERT: G 114 ARG cc_start: 0.8329 (mmm160) cc_final: 0.7740 (mmm-85) outliers start: 194 outliers final: 107 residues processed: 353 average time/residue: 0.6150 time to fit residues: 258.9543 Evaluate side-chains 305 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 174 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 138 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR 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 40 PHE Chi-restraints excluded: chain C residue 65 LYS 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 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 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 506 THR 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 649 GLU 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 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 167 MET 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 68 SER 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 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 E residue 12 LEU 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 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: 10.0000 chunk 356 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 288 optimal weight: 50.0000 chunk 95 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 389 ASN ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.058842 restraints weight = 65436.068| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.41 r_work: 0.2597 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30181 Z= 0.187 Angle : 0.614 11.163 41287 Z= 0.323 Chirality : 0.045 0.313 4712 Planarity : 0.005 0.133 5119 Dihedral : 13.881 85.487 4924 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.25 % Favored : 92.49 % Rotamer: Outliers : 5.99 % Allowed : 31.58 % 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: -1.06 (0.14), residues: 3515 helix: 1.55 (0.18), residues: 954 sheet: -0.59 (0.22), residues: 602 loop : -2.01 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 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 0.00448 / 0.19 (30173) covalent geometry : angle 0.61208 / 0.32 (41275) hydrogen bonds : bond 0.04898 / 3.37 ( 1047) hydrogen bonds : angle 4.50988 / 3.07 ( 2818) metal coordination : bond 0.01189 / 0.63 ( 8) metal coordination : angle 3.10930 / 1.69 ( 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 359 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 180 time to evaluate : 1.141 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: 0.8998 (t0) cc_final: 0.8648 (t0) REVERT: A 204 SER cc_start: 0.7767 (OUTLIER) cc_final: 0.7388 (t) REVERT: B 61 ASN cc_start: 0.8692 (t0) cc_final: 0.8372 (t0) REVERT: B 116 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: C 38 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7634 (mm-30) REVERT: C 40 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7736 (p90) REVERT: C 163 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: C 306 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8972 (mm) REVERT: C 309 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8584 (mp) REVERT: C 563 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9118 (t) REVERT: C 604 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: C 649 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: C 726 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8351 (pp) REVERT: C 780 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: D 46 TYR cc_start: 0.8306 (t80) cc_final: 0.7527 (t80) REVERT: D 47 ARG cc_start: 0.9018 (ttm170) cc_final: 0.8541 (tpp-160) REVERT: D 167 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9232 (mmm) REVERT: D 168 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8892 (pp20) REVERT: D 174 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: Z 91 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: Z 164 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8416 (mp) REVERT: Z 212 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: Z 269 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: Z 299 ARG cc_start: 0.8219 (ppt170) cc_final: 0.7979 (ppt170) REVERT: Z 366 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7848 (tm) REVERT: Z 643 LYS cc_start: 0.4394 (OUTLIER) cc_final: 0.2974 (tmmt) REVERT: Z 669 GLN cc_start: 0.5447 (OUTLIER) cc_final: 0.4896 (pm20) REVERT: Z 683 LEU cc_start: -0.0326 (OUTLIER) cc_final: -0.2339 (pp) REVERT: Z 804 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.4066 (tt0) REVERT: Z 838 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (pt) REVERT: Z 1033 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: Z 1141 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: Z 1146 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8790 (pp) REVERT: Z 1154 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: G 47 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7248 (mm) REVERT: G 77 GLU cc_start: 0.6595 (mp0) cc_final: 0.6066 (mp0) REVERT: G 78 LYS cc_start: 0.8982 (mppt) cc_final: 0.8328 (mtpt) REVERT: G 92 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8574 (t0) REVERT: G 113 LYS cc_start: 0.8623 (tmmt) cc_final: 0.8394 (tmmt) REVERT: G 114 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7661 (mmm-85) outliers start: 179 outliers final: 105 residues processed: 341 average time/residue: 0.6031 time to fit residues: 245.5189 Evaluate side-chains 306 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 171 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 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 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 93 THR 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 164 THR 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 306 ILE 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 342 VAL 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 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 620 CYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 GLU 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 929 VAL 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 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 167 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 395 HIS 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 608 THR Chi-restraints excluded: chain D residue 620 THR 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 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 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 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 E residue 12 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 295 optimal weight: 30.0000 chunk 291 optimal weight: 30.0000 chunk 42 optimal weight: 0.0980 chunk 284 optimal weight: 0.8980 chunk 278 optimal weight: 50.0000 chunk 252 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.106400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060549 restraints weight = 65174.836| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.45 r_work: 0.2638 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30181 Z= 0.118 Angle : 0.597 18.380 41287 Z= 0.310 Chirality : 0.043 0.368 4712 Planarity : 0.005 0.164 5119 Dihedral : 13.764 84.582 4920 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.66 % Favored : 93.09 % Rotamer: Outliers : 4.75 % Allowed : 32.95 % 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: -0.90 (0.14), residues: 3515 helix: 1.68 (0.18), residues: 952 sheet: -0.44 (0.22), residues: 608 loop : -1.92 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 152 TYR 0.012 0.001 TYR Z1024 PHE 0.020 0.001 PHE A 3 TRP 0.037 0.001 TRP Z 728 HIS 0.008 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (30173) covalent geometry : angle 0.59494 / 0.31 (41275) hydrogen bonds : bond 0.03847 / 2.66 ( 1047) hydrogen bonds : angle 4.38889 / 2.98 ( 2818) metal coordination : bond 0.00629 / 0.32 ( 8) metal coordination : angle 2.87871 / 1.61 ( 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 327 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 185 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8858 (t) REVERT: A 112 ASP cc_start: 0.9005 (t0) cc_final: 0.8629 (t0) REVERT: A 150 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 204 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.7215 (t) REVERT: B 61 ASN cc_start: 0.8682 (t0) cc_final: 0.8369 (t0) REVERT: B 116 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: B 138 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: B 150 ILE cc_start: 0.8531 (tp) cc_final: 0.8158 (tp) REVERT: C 38 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7652 (mm-30) REVERT: C 40 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7238 (p90) REVERT: C 163 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: C 563 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9078 (t) REVERT: C 604 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8722 (mmmm) REVERT: C 649 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: C 726 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8367 (pp) REVERT: D 46 TYR cc_start: 0.8269 (t80) cc_final: 0.7471 (t80) REVERT: D 47 ARG cc_start: 0.9028 (ttm170) cc_final: 0.8549 (tpp-160) REVERT: D 77 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7917 (ttp80) REVERT: D 167 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9212 (mmm) REVERT: D 174 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8605 (m-10) REVERT: Z 91 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: Z 212 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8731 (pt0) REVERT: Z 269 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: Z 299 ARG cc_start: 0.8200 (ppt170) cc_final: 0.7952 (ppt170) REVERT: Z 366 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7797 (tm) REVERT: Z 643 LYS cc_start: 0.4009 (OUTLIER) cc_final: 0.2635 (tmmm) REVERT: Z 669 GLN cc_start: 0.5328 (OUTLIER) cc_final: 0.4757 (mp10) REVERT: Z 683 LEU cc_start: -0.0589 (OUTLIER) cc_final: -0.2509 (pp) REVERT: Z 838 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (pt) REVERT: Z 1146 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8802 (pp) REVERT: Z 1154 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: G 45 GLN cc_start: 0.8984 (pp30) cc_final: 0.8487 (pp30) REVERT: G 92 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8546 (t70) REVERT: G 113 LYS cc_start: 0.8664 (tmmt) cc_final: 0.8418 (tmmt) REVERT: G 114 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7673 (mmm-85) outliers start: 142 outliers final: 81 residues processed: 308 average time/residue: 0.6778 time to fit residues: 247.3946 Evaluate side-chains 280 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 175 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 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 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 93 THR 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 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 342 VAL 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 603 GLU Chi-restraints excluded: chain C residue 604 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 649 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 944 VAL 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 167 MET Chi-restraints excluded: chain D residue 174 TYR 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 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 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 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 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: 0.9990 chunk 325 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 174 optimal weight: 0.0870 chunk 101 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.107015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062416 restraints weight = 65624.871| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.18 r_work: 0.2712 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30181 Z= 0.120 Angle : 0.595 13.614 41287 Z= 0.309 Chirality : 0.043 0.323 4712 Planarity : 0.005 0.145 5119 Dihedral : 13.718 83.570 4911 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.83 % Favored : 92.92 % Rotamer: Outliers : 4.22 % Allowed : 33.79 % Favored : 61.99 % 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: -0.83 (0.14), residues: 3515 helix: 1.73 (0.18), residues: 951 sheet: -0.29 (0.22), residues: 600 loop : -1.91 (0.13), residues: 1964 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 0.031 0.001 TRP Z 728 HIS 0.009 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30173) covalent geometry : angle 0.59307 / 0.31 (41275) hydrogen bonds : bond 0.03782 / 2.61 ( 1047) hydrogen bonds : angle 4.33991 / 2.96 ( 2818) metal coordination : bond 0.00652 / 0.33 ( 8) metal coordination : angle 2.71619 / 1.52 ( 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 312 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 186 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9037 (t) REVERT: A 112 ASP cc_start: 0.9018 (t0) cc_final: 0.8681 (t0) REVERT: A 204 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7628 (t) REVERT: B 61 ASN cc_start: 0.8823 (t0) cc_final: 0.8537 (t0) REVERT: B 138 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: C 38 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7765 (mm-30) REVERT: C 40 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7096 (p90) REVERT: C 139 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 163 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: C 178 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8157 (mmm-85) REVERT: C 563 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9157 (t) REVERT: C 604 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8885 (mmmm) REVERT: C 726 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8623 (pp) REVERT: D 46 TYR cc_start: 0.8382 (t80) cc_final: 0.7866 (t80) REVERT: D 47 ARG cc_start: 0.9003 (ttm170) cc_final: 0.8606 (tpp-160) REVERT: D 167 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9185 (mmm) REVERT: D 174 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: Z 91 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: Z 212 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8785 (pt0) REVERT: Z 269 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: Z 366 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7823 (tm) REVERT: Z 525 MET cc_start: 0.5656 (pmm) cc_final: 0.4285 (ppp) REVERT: Z 643 LYS cc_start: 0.3864 (OUTLIER) cc_final: 0.2392 (tmmm) REVERT: Z 669 GLN cc_start: 0.5250 (OUTLIER) cc_final: 0.4638 (mp10) REVERT: Z 683 LEU cc_start: -0.0709 (OUTLIER) cc_final: -0.2629 (pp) REVERT: Z 804 GLU cc_start: 0.4558 (OUTLIER) cc_final: 0.4140 (tt0) REVERT: Z 1146 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8770 (pp) REVERT: Z 1154 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: Z 1170 MET cc_start: 0.8153 (mpm) cc_final: 0.7928 (mpm) REVERT: G 45 GLN cc_start: 0.9018 (pp30) cc_final: 0.8536 (pp30) REVERT: G 92 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8669 (t70) REVERT: G 113 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8506 (tmmt) REVERT: G 114 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7634 (mmm-85) outliers start: 126 outliers final: 83 residues processed: 297 average time/residue: 0.6913 time to fit residues: 243.0317 Evaluate side-chains 277 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 173 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL 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 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 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 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 93 THR 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 164 THR Chi-restraints excluded: chain C residue 200 LEU 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 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 839 GLU Chi-restraints excluded: chain C residue 944 VAL 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 88 CYS Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 509 SER 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 516 THR 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 308 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 302 optimal weight: 9.9990 chunk 217 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.059999 restraints weight = 66111.411| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.16 r_work: 0.2663 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 30181 Z= 0.236 Angle : 0.653 12.084 41287 Z= 0.340 Chirality : 0.046 0.314 4712 Planarity : 0.005 0.135 5119 Dihedral : 13.806 82.649 4911 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.51 % Favored : 92.20 % Rotamer: Outliers : 4.48 % Allowed : 33.46 % Favored : 62.06 % 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: -0.94 (0.14), residues: 3515 helix: 1.60 (0.18), residues: 957 sheet: -0.39 (0.22), residues: 579 loop : -1.94 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 178 TYR 0.014 0.001 TYR Z 50 PHE 0.022 0.001 PHE A 3 TRP 0.032 0.001 TRP Z 728 HIS 0.013 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (30173) covalent geometry : angle 0.65125 / 0.34 (41275) hydrogen bonds : bond 0.05124 / 3.52 ( 1047) hydrogen bonds : angle 4.43889 / 3.04 ( 2818) metal coordination : bond 0.01317 / 0.71 ( 8) metal coordination : angle 2.95053 / 1.59 ( 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 300 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 166 time to evaluate : 1.203 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 204 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7769 (t) REVERT: B 61 ASN cc_start: 0.8832 (t0) cc_final: 0.8556 (t0) REVERT: B 150 ILE cc_start: 0.8697 (tp) cc_final: 0.8309 (tp) REVERT: C 38 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 40 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7036 (p90) REVERT: C 139 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 178 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8272 (mmp80) REVERT: C 563 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9206 (t) REVERT: C 604 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8898 (mmmm) REVERT: D 46 TYR cc_start: 0.8449 (t80) cc_final: 0.7955 (t80) REVERT: D 47 ARG cc_start: 0.9014 (ttm170) cc_final: 0.8605 (tpp-160) REVERT: D 77 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: D 167 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9217 (mmm) REVERT: D 168 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8894 (pp20) REVERT: D 174 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: D 265 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8420 (ttp-170) REVERT: Z 91 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: Z 212 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: Z 269 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: Z 366 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7898 (tm) REVERT: Z 643 LYS cc_start: 0.3789 (OUTLIER) cc_final: 0.2238 (tmmm) REVERT: Z 669 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4533 (pm20) REVERT: Z 683 LEU cc_start: -0.0823 (OUTLIER) cc_final: -0.2713 (pp) REVERT: Z 804 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.4178 (tt0) REVERT: Z 1146 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8714 (pp) REVERT: Z 1154 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: Z 1170 MET cc_start: 0.8251 (mpm) cc_final: 0.8032 (mpm) REVERT: G 45 GLN cc_start: 0.9037 (pp30) cc_final: 0.8575 (pp30) REVERT: G 92 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8668 (t70) REVERT: G 114 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7748 (mmm160) outliers start: 134 outliers final: 92 residues processed: 285 average time/residue: 0.6759 time to fit residues: 227.6311 Evaluate side-chains 284 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 173 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 85 VAL 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 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 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 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 93 THR 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 164 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 264 LEU 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 342 VAL 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 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 944 VAL Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1010 VAL 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 509 SER 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 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 592 ILE 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 346 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 273 optimal weight: 40.0000 chunk 90 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 915 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.061299 restraints weight = 65397.866| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.16 r_work: 0.2693 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 30181 Z= 0.134 Angle : 0.627 12.716 41287 Z= 0.326 Chirality : 0.044 0.301 4712 Planarity : 0.005 0.134 5119 Dihedral : 13.777 83.956 4911 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.71 % Favored : 93.00 % Rotamer: Outliers : 3.65 % Allowed : 34.23 % 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: -0.83 (0.14), residues: 3515 helix: 1.73 (0.18), residues: 951 sheet: -0.26 (0.22), residues: 579 loop : -1.90 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Z1016 TYR 0.010 0.001 TYR C 680 PHE 0.020 0.001 PHE A 3 TRP 0.033 0.001 TRP Z 728 HIS 0.008 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (30173) covalent geometry : angle 0.62539 / 0.33 (41275) hydrogen bonds : bond 0.04203 / 2.90 ( 1047) hydrogen bonds : angle 4.33201 / 2.96 ( 2818) metal coordination : bond 0.00793 / 0.41 ( 8) metal coordination : angle 2.97378 / 1.64 ( 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 291 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 182 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8205 (tpp-160) REVERT: A 85 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9043 (t) REVERT: A 112 ASP cc_start: 0.9038 (t0) cc_final: 0.8700 (t0) REVERT: A 204 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7707 (t) REVERT: B 61 ASN cc_start: 0.8840 (t0) cc_final: 0.8580 (t0) REVERT: B 110 ASP cc_start: 0.8971 (m-30) cc_final: 0.8402 (m-30) REVERT: B 150 ILE cc_start: 0.8707 (tp) cc_final: 0.8297 (tp) REVERT: C 38 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 40 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 178 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8312 (mmp80) REVERT: C 563 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9131 (t) REVERT: C 604 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8878 (mmmm) REVERT: D 46 TYR cc_start: 0.8425 (t80) cc_final: 0.7917 (t80) REVERT: D 47 ARG cc_start: 0.9012 (ttm170) cc_final: 0.8607 (tpp-160) REVERT: D 77 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7999 (ttp80) REVERT: D 167 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9190 (mmm) REVERT: D 174 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8440 (m-10) REVERT: Z 91 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: Z 212 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8814 (pt0) REVERT: Z 269 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: Z 366 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7917 (tm) REVERT: Z 525 MET cc_start: 0.5611 (pmm) cc_final: 0.4238 (ppp) REVERT: Z 643 LYS cc_start: 0.3591 (OUTLIER) cc_final: 0.2251 (tmmm) REVERT: Z 669 GLN cc_start: 0.5217 (OUTLIER) cc_final: 0.4557 (pm20) REVERT: Z 683 LEU cc_start: -0.1046 (OUTLIER) cc_final: -0.2863 (pp) REVERT: Z 804 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.4162 (tt0) REVERT: Z 1146 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8710 (pp) REVERT: Z 1154 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: Z 1170 MET cc_start: 0.8292 (mpm) cc_final: 0.8083 (mpm) REVERT: G 45 GLN cc_start: 0.9025 (pp30) cc_final: 0.8568 (pp30) REVERT: G 52 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: G 114 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7946 (mmm-85) outliers start: 109 outliers final: 84 residues processed: 277 average time/residue: 0.6902 time to fit residues: 226.1209 Evaluate side-chains 278 residues out of total 2989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 177 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 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 138 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 THR 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 40 PHE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 93 THR 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 164 THR 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 369 SER 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 944 VAL Chi-restraints excluded: chain C residue 972 THR 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 167 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 509 SER 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 351 GLU Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 445 VAL 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 592 ILE 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 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 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 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 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 281 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060820 restraints weight = 66128.217| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.19 r_work: 0.2684 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2401 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= 0.163 Angle : 0.641 23.701 41287 Z= 0.330 Chirality : 0.044 0.360 4712 Planarity : 0.005 0.180 5119 Dihedral : 13.770 83.294 4910 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.97 % Favored : 92.75 % Rotamer: Outliers : 3.85 % Allowed : 34.02 % Favored : 62.13 % 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: -0.85 (0.14), residues: 3515 helix: 1.70 (0.18), residues: 955 sheet: -0.32 (0.22), residues: 579 loop : -1.90 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG Z1016 TYR 0.011 0.001 TYR Z 50 PHE 0.020 0.001 PHE A 3 TRP 0.034 0.001 TRP Z 728 HIS 0.009 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (30173) covalent geometry : angle 0.63877 / 0.33 (41275) hydrogen bonds : bond 0.04391 / 3.02 ( 1047) hydrogen bonds : angle 4.34370 / 2.97 ( 2818) metal coordination : bond 0.00936 / 0.49 ( 8) metal coordination : angle 2.92395 / 1.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11153.18 seconds wall clock time: 190 minutes 19.54 seconds (11419.54 seconds total)