Starting phenix.real_space_refine on Mon Sep 14 19:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ubm_26438/09_2026/7ubm_26438.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1440 atoms to isotropic. 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 3 6.06 5 P 115 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 19434 2.51 5 N 5603 2.21 5 O 6294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31583 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1096 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Chain: "2" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1052 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2900 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 5, 'TRANS': 347} Chain breaks: 3 Chain: "Q" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1250 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "R" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNAv2': 11} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" 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 16727 SG CYS D 70 67.235 116.284 80.400 1.00 65.16 S ATOM 16741 SG CYS D 72 68.958 119.421 79.405 1.00 68.07 S ATOM 16849 SG CYS D 85 66.303 118.016 77.155 1.00 70.14 S ATOM 16873 SG CYS D 88 69.576 116.194 77.335 1.00 63.96 S ATOM 22561 SG CYS D 814 65.941 48.347 72.904 1.00 85.18 S ATOM 23126 SG CYS D 888 68.045 51.245 74.109 1.00 75.57 S ATOM 23177 SG CYS D 895 65.650 49.511 76.530 1.00 68.20 S ATOM 23198 SG CYS D 898 68.736 47.727 75.407 1.00 69.54 S ATOM 30648 SG CYS Q 118 55.115 115.998 66.693 1.00101.82 S ATOM 30673 SG CYS Q 121 56.575 117.258 69.922 1.00 99.29 S ATOM 30851 SG CYS Q 144 55.098 119.839 67.532 1.00125.92 S ATOM 30872 SG CYS Q 147 52.876 117.471 69.391 1.00129.58 S Time building chain proxies: 6.37, per 1000 atoms: 0.20 Number of scatterers: 31583 At special positions: 0 Unit cell: (167.362, 159.9, 172.692, 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 3 29.99 S 133 16.00 P 115 15.00 Mg 1 11.99 O 6294 8.00 N 5603 7.00 C 19434 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb=" ZN Q1500 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 147 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 121 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 144 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 118 " Number of angles added : 18 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 47 sheets defined 43.1% alpha, 14.2% beta 47 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.432A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.974A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.682A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.695A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.153A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.222A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.525A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.038A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 removed outlier: 4.250A pdb=" N LEU C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.503A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.564A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 3.538A pdb=" N VAL C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.018A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.641A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.625A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.684A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.582A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.842A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.632A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 704 removed outlier: 3.528A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.063A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.716A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.991A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.342A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 112 through 136 removed outlier: 4.069A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 157 through 160 removed outlier: 3.911A pdb=" N ASP F 160 " --> pdb=" O ARG F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 160' Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.545A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 293 removed outlier: 3.557A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 305 Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 329 through 332 removed outlier: 4.473A pdb=" N ASP F 332 " --> pdb=" O LYS F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 332' Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 4.025A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.568A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.505A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 447 removed outlier: 4.234A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.842A pdb=" N VAL F 576 " --> pdb=" O THR F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 599 removed outlier: 3.961A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 56 Processing helix chain 'Q' and resid 61 through 78 removed outlier: 4.025A pdb=" N LYS Q 65 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 81 No H-bonds generated for 'chain 'Q' and resid 79 through 81' Processing helix chain 'Q' and resid 88 through 109 removed outlier: 3.590A pdb=" N LYS Q 92 " --> pdb=" O GLU Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 137 Processing helix chain 'Q' and resid 156 through 165 removed outlier: 4.423A pdb=" N ALA Q 160 " --> pdb=" O PRO Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 179 Processing helix chain 'Q' and resid 179 through 207 removed outlier: 4.006A pdb=" N LEU Q 183 " --> pdb=" O THR Q 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL Q 205 " --> pdb=" O ILE Q 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.377A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.471A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.791A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 4.857A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.323A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.523A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.064A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.367A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.958A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.508A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.621A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.989A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C 335 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 250 through 251 removed outlier: 4.443A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.736A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 4.966A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.543A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.703A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.749A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.368A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.502A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.239A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.314A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 5.087A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.143A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.508A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.458A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE6, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.719A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1048 Processing sheet with id=AE8, first strand: chain 'D' and resid 1174 through 1178 removed outlier: 7.140A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D1166 " --> pdb=" O ARG D1174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.656A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 162 through 164 removed outlier: 3.658A pdb=" N ARG F 260 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 127 through 128 1337 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 7.86 Time building geometry restraints manager: 3.20 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: 9076 1.33 - 1.46: 6164 1.46 - 1.58: 16601 1.58 - 1.70: 227 1.70 - 1.82: 228 Bond restraints: 32296 Sorted by residual: bond pdb=" C GLU B 193 " pdb=" N GLN B 194 " ideal model delta sigma weight residual 1.331 1.269 0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1' DT 1 3 " pdb=" N1 DT 1 3 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C3' DG 2 13 " pdb=" O3' DG 2 13 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C3' DT 2 39 " pdb=" C2' DT 2 39 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA 2 16 " pdb=" O3' DA 2 16 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 ... (remaining 32291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 42472 1.98 - 3.96: 1438 3.96 - 5.93: 116 5.93 - 7.91: 44 7.91 - 9.89: 24 Bond angle restraints: 44094 Sorted by residual: angle pdb=" O4' DT 2 14 " pdb=" C4' DT 2 14 " pdb=" C3' DT 2 14 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.96e+01 angle pdb=" O4' DT 2 15 " pdb=" C4' DT 2 15 " pdb=" C3' DT 2 15 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" C VAL D1027 " pdb=" N ILE D1028 " pdb=" CA ILE D1028 " ideal model delta sigma weight residual 120.49 127.42 -6.93 1.38e+00 5.25e-01 2.52e+01 angle pdb=" N3 DT 2 21 " pdb=" C4 DT 2 21 " pdb=" O4 DT 2 21 " ideal model delta sigma weight residual 119.90 122.85 -2.95 6.00e-01 2.78e+00 2.41e+01 angle pdb=" O4' DT 2 19 " pdb=" C4' DT 2 19 " pdb=" C3' DT 2 19 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 ... (remaining 44089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 17985 28.27 - 56.54: 1425 56.54 - 84.81: 155 84.81 - 113.08: 10 113.08 - 141.35: 1 Dihedral angle restraints: 19576 sinusoidal: 8885 harmonic: 10691 Sorted by residual: dihedral pdb=" O5' G R 2 " pdb=" C5' G R 2 " pdb=" C4' G R 2 " pdb=" C3' G R 2 " ideal model delta sinusoidal sigma weight residual 180.00 127.32 52.68 3 6.40e+00 2.44e-02 5.02e+01 dihedral pdb=" CA ARG D 346 " pdb=" C ARG D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4586 0.094 - 0.189: 402 0.189 - 0.283: 22 0.283 - 0.378: 1 0.378 - 0.472: 2 Chirality restraints: 5013 Sorted by residual: chirality pdb=" CA GLU B 193 " pdb=" N GLU B 193 " pdb=" C GLU B 193 " pdb=" CB GLU B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB ILE D 707 " pdb=" CA ILE D 707 " pdb=" CG1 ILE D 707 " pdb=" CG2 ILE D 707 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" P G R 3 " pdb=" OP1 G R 3 " pdb=" OP2 G R 3 " pdb=" O5' G R 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5010 not shown) Planarity restraints: 5355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 192 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C VAL B 192 " -0.081 2.00e-02 2.50e+03 pdb=" O VAL B 192 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU B 193 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 504 " -0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C GLN D 504 " 0.078 2.00e-02 2.50e+03 pdb=" O GLN D 504 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 505 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 520 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.049 5.00e-02 4.00e+02 ... (remaining 5352 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 465 2.64 - 3.20: 26207 3.20 - 3.77: 52312 3.77 - 4.33: 69211 4.33 - 4.90: 111883 Nonbonded interactions: 260078 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.085 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1503 " model vdw 2.172 2.170 nonbonded pdb=" O MET D 724 " pdb=" OG SER D 728 " model vdw 2.287 3.040 ... (remaining 260073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 35.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 32308 Z= 0.309 Angle : 0.835 9.891 44112 Z= 0.517 Chirality : 0.054 0.472 5013 Planarity : 0.007 0.089 5355 Dihedral : 18.695 141.349 12692 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 4.08 % Allowed : 15.41 % Favored : 80.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.11), residues: 3692 helix: -2.23 (0.10), residues: 1513 sheet: -1.74 (0.25), residues: 361 loop : -2.51 (0.12), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 346 TYR 0.016 0.002 TYR C 47 PHE 0.017 0.002 PHE D 338 TRP 0.011 0.001 TRP D 33 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.31 (32296) covalent geometry : angle 0.83400 / 0.52 (44094) hydrogen bonds : bond 0.12779 / 14.90 ( 1445) hydrogen bonds : angle 6.67340 / 8.01 ( 4087) metal coordination : bond 0.00577 / 0.53 ( 12) metal coordination : angle 2.27359 / 2.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 434 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8382 (ptpp) REVERT: B 125 LYS cc_start: 0.9224 (mttm) cc_final: 0.8959 (tttm) REVERT: C 165 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6796 (t-170) REVERT: C 292 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8867 (mp) REVERT: C 301 TYR cc_start: 0.7749 (m-10) cc_final: 0.7308 (m-10) REVERT: C 422 LYS cc_start: 0.8836 (mppt) cc_final: 0.8542 (mttt) REVERT: C 546 GLU cc_start: 0.6956 (tt0) cc_final: 0.6159 (mm-30) REVERT: C 841 ARG cc_start: 0.6955 (mmm160) cc_final: 0.6296 (mtm110) REVERT: C 949 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7021 (tm-30) REVERT: C 950 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 953 LEU cc_start: 0.9169 (mt) cc_final: 0.8842 (mt) REVERT: C 1034 ARG cc_start: 0.8811 (ptm-80) cc_final: 0.8436 (ttp80) REVERT: C 1243 MET cc_start: 0.8395 (ttp) cc_final: 0.8158 (ttp) REVERT: D 49 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: D 129 ASP cc_start: 0.7792 (t0) cc_final: 0.7545 (t70) REVERT: D 151 MET cc_start: 0.7233 (pmm) cc_final: 0.7012 (pmm) REVERT: D 174 ASP cc_start: 0.8055 (m-30) cc_final: 0.7831 (t0) REVERT: D 196 GLN cc_start: 0.8856 (tt0) cc_final: 0.8146 (tm-30) REVERT: D 399 LYS cc_start: 0.7651 (pptt) cc_final: 0.7206 (tptp) REVERT: D 411 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8502 (mm) REVERT: D 504 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: D 678 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8122 (ttt-90) REVERT: D 1021 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6294 (p0) REVERT: E 49 ILE cc_start: 0.8585 (mt) cc_final: 0.8335 (mt) REVERT: E 53 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7799 (mt-10) REVERT: Q 71 MET cc_start: 0.8230 (tpt) cc_final: 0.7955 (tpt) REVERT: Q 136 TRP cc_start: 0.8388 (m100) cc_final: 0.8067 (m100) REVERT: Q 155 MET cc_start: 0.8229 (ttp) cc_final: 0.7733 (ttp) REVERT: Q 166 MET cc_start: 0.7746 (ppp) cc_final: 0.7111 (ppp) outliers start: 129 outliers final: 77 residues processed: 556 average time/residue: 0.2240 time to fit residues: 194.6933 Evaluate side-chains 417 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 333 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1302 THR Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain Q residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 186 ASN B 103 ASN C 219 GLN C 330 HIS C 447 HIS C 517 GLN C 518 ASN C 618 GLN C 799 ASN C1008 GLN C1136 GLN C1220 GLN C1313 HIS D 80 HIS D 157 GLN D 196 GLN D 232 ASN D 294 ASN D 450 HIS D 777 HIS D 792 ASN D 897 HIS ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN D1114 GLN D1249 ASN D1259 GLN D1326 GLN E 43 ASN E 61 ASN E 70 GLN F 129 GLN F 271 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 309 ASN F 323 ASN F 406 GLN F 409 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097007 restraints weight = 55684.281| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.77 r_work: 0.2987 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32308 Z= 0.138 Angle : 0.607 9.280 44112 Z= 0.326 Chirality : 0.044 0.215 5013 Planarity : 0.005 0.066 5355 Dihedral : 17.023 141.901 5510 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 18.10 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.12), residues: 3692 helix: -0.39 (0.12), residues: 1501 sheet: -1.69 (0.24), residues: 398 loop : -2.00 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 352 TYR 0.031 0.001 TYR Q 81 PHE 0.031 0.001 PHE Q 73 TRP 0.016 0.002 TRP F 433 HIS 0.011 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (32296) covalent geometry : angle 0.60605 / 0.33 (44094) hydrogen bonds : bond 0.04294 / 4.80 ( 1445) hydrogen bonds : angle 5.21757 / 6.30 ( 4087) metal coordination : bond 0.00312 / 0.34 ( 12) metal coordination : angle 1.91546 / 2.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 366 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7600 (mp10) cc_final: 0.7400 (mp10) REVERT: A 145 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8418 (tttt) REVERT: B 125 LYS cc_start: 0.9363 (mttm) cc_final: 0.8978 (tttm) REVERT: B 197 ASP cc_start: 0.8072 (p0) cc_final: 0.7836 (p0) REVERT: B 226 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: C 165 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7249 (t-170) REVERT: C 299 LYS cc_start: 0.8487 (tptp) cc_final: 0.7916 (tptp) REVERT: C 301 TYR cc_start: 0.8167 (m-10) cc_final: 0.7742 (m-10) REVERT: C 378 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7682 (tpp80) REVERT: C 422 LYS cc_start: 0.8978 (mppt) cc_final: 0.8727 (mttt) REVERT: C 503 LYS cc_start: 0.8416 (tppt) cc_final: 0.8115 (tptt) REVERT: C 546 GLU cc_start: 0.7254 (tt0) cc_final: 0.5989 (mm-30) REVERT: C 841 ARG cc_start: 0.6630 (mmm160) cc_final: 0.5607 (mtm110) REVERT: C 949 GLU cc_start: 0.8704 (tm-30) cc_final: 0.7103 (tm-30) REVERT: C 950 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 953 LEU cc_start: 0.9117 (mt) cc_final: 0.8728 (mt) REVERT: D 129 ASP cc_start: 0.8391 (t0) cc_final: 0.8057 (t70) REVERT: D 151 MET cc_start: 0.7332 (pmm) cc_final: 0.7098 (pmm) REVERT: D 174 ASP cc_start: 0.8260 (m-30) cc_final: 0.7902 (t0) REVERT: D 180 MET cc_start: 0.8777 (mtp) cc_final: 0.8423 (mtp) REVERT: D 196 GLN cc_start: 0.8939 (tt0) cc_final: 0.8682 (tm-30) REVERT: D 284 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (p0) REVERT: D 399 LYS cc_start: 0.7870 (pptt) cc_final: 0.7167 (pptt) REVERT: D 411 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8633 (mm) REVERT: D 504 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: D 545 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8493 (m-70) REVERT: D 709 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5231 (tpm170) REVERT: D 839 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9112 (p) REVERT: E 12 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8294 (mmtm) REVERT: E 49 ILE cc_start: 0.8570 (mt) cc_final: 0.8169 (mt) REVERT: F 137 TYR cc_start: 0.7587 (t80) cc_final: 0.7201 (t80) REVERT: F 294 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: F 425 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: F 433 TRP cc_start: 0.7994 (t60) cc_final: 0.7298 (t60) REVERT: Q 56 HIS cc_start: 0.7286 (m-70) cc_final: 0.7077 (m170) REVERT: Q 155 MET cc_start: 0.8324 (ttp) cc_final: 0.7831 (ttp) REVERT: Q 166 MET cc_start: 0.8200 (ppp) cc_final: 0.7563 (ppp) outliers start: 100 outliers final: 61 residues processed: 451 average time/residue: 0.2082 time to fit residues: 149.8456 Evaluate side-chains 402 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 331 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 374 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 259 optimal weight: 0.1980 chunk 334 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN E 62 GLN F 271 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 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 = 0.4041 r_free = 0.4041 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094869 restraints weight = 55725.309| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.86 r_work: 0.2948 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32308 Z= 0.212 Angle : 0.626 9.958 44112 Z= 0.331 Chirality : 0.045 0.231 5013 Planarity : 0.005 0.067 5355 Dihedral : 16.856 141.986 5439 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.51 % Allowed : 18.44 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.36 (0.13), residues: 3692 helix: 0.23 (0.13), residues: 1512 sheet: -1.44 (0.24), residues: 406 loop : -1.79 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 836 TYR 0.019 0.001 TYR F 148 PHE 0.023 0.001 PHE D 176 TRP 0.008 0.001 TRP D1020 HIS 0.007 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (32296) covalent geometry : angle 0.62389 / 0.33 (44094) hydrogen bonds : bond 0.04388 / 4.88 ( 1445) hydrogen bonds : angle 4.96771 / 5.99 ( 4087) metal coordination : bond 0.00690 / 0.64 ( 12) metal coordination : angle 2.36649 / 2.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 345 time to evaluate : 1.146 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: B 125 LYS cc_start: 0.9340 (mttm) cc_final: 0.8979 (tttm) REVERT: B 132 HIS cc_start: 0.8664 (m-70) cc_final: 0.8309 (m-70) REVERT: B 197 ASP cc_start: 0.7805 (p0) cc_final: 0.7578 (p0) REVERT: B 226 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: C 299 LYS cc_start: 0.8502 (tptp) cc_final: 0.7955 (tptp) REVERT: C 301 TYR cc_start: 0.8177 (m-10) cc_final: 0.7802 (m-10) REVERT: C 343 HIS cc_start: 0.8503 (m90) cc_final: 0.8219 (m90) REVERT: C 422 LYS cc_start: 0.8970 (mppt) cc_final: 0.8739 (mttt) REVERT: C 546 GLU cc_start: 0.7375 (tt0) cc_final: 0.6085 (mm-30) REVERT: C 783 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8853 (mt) REVERT: C 841 ARG cc_start: 0.6729 (mmm160) cc_final: 0.5780 (mtm110) REVERT: C 949 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 996 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8028 (mtm110) REVERT: C 1028 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8998 (mtmm) REVERT: C 1034 ARG cc_start: 0.8909 (tmm-80) cc_final: 0.8649 (ttp80) REVERT: C 1233 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9147 (mt) REVERT: D 129 ASP cc_start: 0.8342 (t0) cc_final: 0.8024 (t70) REVERT: D 151 MET cc_start: 0.7477 (pmm) cc_final: 0.7225 (pmm) REVERT: D 174 ASP cc_start: 0.8207 (m-30) cc_final: 0.7947 (t0) REVERT: D 180 MET cc_start: 0.8803 (mtp) cc_final: 0.8465 (mtp) REVERT: D 196 GLN cc_start: 0.8936 (tt0) cc_final: 0.8734 (tm-30) REVERT: D 229 GLN cc_start: 0.8617 (mt0) cc_final: 0.8417 (mt0) REVERT: D 284 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7818 (p0) REVERT: D 411 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 504 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: D 709 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5250 (tpm170) REVERT: E 62 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: F 137 TYR cc_start: 0.7533 (t80) cc_final: 0.7041 (t80) REVERT: F 277 MET cc_start: 0.8747 (ptp) cc_final: 0.7932 (tpp) REVERT: F 425 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: F 433 TRP cc_start: 0.8158 (t60) cc_final: 0.7527 (t60) REVERT: Q 49 MET cc_start: 0.7387 (tpt) cc_final: 0.7018 (tpp) REVERT: Q 96 LEU cc_start: 0.9684 (mp) cc_final: 0.9222 (tp) REVERT: Q 155 MET cc_start: 0.8295 (ttp) cc_final: 0.7797 (ttp) REVERT: Q 166 MET cc_start: 0.8245 (ppp) cc_final: 0.7635 (ppp) outliers start: 111 outliers final: 68 residues processed: 439 average time/residue: 0.2057 time to fit residues: 146.3984 Evaluate side-chains 392 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1089 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 52 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 45 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN F 271 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096157 restraints weight = 55167.007| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.76 r_work: 0.2982 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32308 Z= 0.140 Angle : 0.578 10.816 44112 Z= 0.306 Chirality : 0.044 0.282 5013 Planarity : 0.004 0.063 5355 Dihedral : 16.724 142.372 5431 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 19.23 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.96 (0.13), residues: 3692 helix: 0.63 (0.13), residues: 1508 sheet: -1.35 (0.24), residues: 399 loop : -1.59 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 274 TYR 0.015 0.001 TYR F 228 PHE 0.023 0.001 PHE C1025 TRP 0.019 0.001 TRP Q 176 HIS 0.010 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (32296) covalent geometry : angle 0.57599 / 0.31 (44094) hydrogen bonds : bond 0.03962 / 4.45 ( 1445) hydrogen bonds : angle 4.79771 / 5.82 ( 4087) metal coordination : bond 0.00431 / 0.42 ( 12) metal coordination : angle 2.43785 / 2.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 349 time to evaluate : 1.329 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 145 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8597 (tttm) REVERT: B 41 ASN cc_start: 0.8755 (t0) cc_final: 0.8540 (t0) REVERT: B 125 LYS cc_start: 0.9366 (mttm) cc_final: 0.8986 (tttm) REVERT: B 132 HIS cc_start: 0.8672 (m-70) cc_final: 0.8335 (m-70) REVERT: B 145 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8274 (tttt) REVERT: B 197 ASP cc_start: 0.7728 (p0) cc_final: 0.7517 (p0) REVERT: C 299 LYS cc_start: 0.8512 (tptp) cc_final: 0.8025 (tptp) REVERT: C 301 TYR cc_start: 0.8128 (m-10) cc_final: 0.7810 (m-10) REVERT: C 311 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7610 (t) REVERT: C 343 HIS cc_start: 0.8554 (m90) cc_final: 0.8286 (m90) REVERT: C 422 LYS cc_start: 0.8939 (mppt) cc_final: 0.8736 (mttt) REVERT: C 517 GLN cc_start: 0.8668 (pt0) cc_final: 0.8435 (pt0) REVERT: C 546 GLU cc_start: 0.7304 (tt0) cc_final: 0.6043 (mm-30) REVERT: C 783 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8800 (mt) REVERT: C 841 ARG cc_start: 0.6492 (mmm160) cc_final: 0.5476 (mtm110) REVERT: C 856 ASN cc_start: 0.7685 (m-40) cc_final: 0.7479 (m-40) REVERT: C 876 GLU cc_start: 0.7725 (tp30) cc_final: 0.7509 (mm-30) REVERT: C 949 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8440 (tm-30) REVERT: C 996 ARG cc_start: 0.8366 (mtm110) cc_final: 0.7906 (mtm110) REVERT: C 1028 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8991 (mtmm) REVERT: C 1034 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8585 (ttp80) REVERT: C 1151 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 1233 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9119 (mt) REVERT: D 129 ASP cc_start: 0.8280 (t0) cc_final: 0.7966 (t70) REVERT: D 151 MET cc_start: 0.7555 (pmm) cc_final: 0.7244 (pmm) REVERT: D 174 ASP cc_start: 0.8212 (m-30) cc_final: 0.7968 (t0) REVERT: D 180 MET cc_start: 0.8749 (mtp) cc_final: 0.8444 (mtp) REVERT: D 284 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7741 (p0) REVERT: D 411 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8695 (mm) REVERT: D 504 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: D 698 MET cc_start: 0.8702 (tpt) cc_final: 0.8157 (mmm) REVERT: F 137 TYR cc_start: 0.7520 (t80) cc_final: 0.7073 (t80) REVERT: F 297 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.3376 (ppp) REVERT: F 425 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: F 433 TRP cc_start: 0.8180 (t60) cc_final: 0.7543 (t60) REVERT: F 571 TYR cc_start: 0.5878 (m-80) cc_final: 0.5494 (m-80) REVERT: Q 49 MET cc_start: 0.7559 (tpt) cc_final: 0.7171 (tpp) REVERT: Q 71 MET cc_start: 0.8298 (tpt) cc_final: 0.7841 (tpt) REVERT: Q 96 LEU cc_start: 0.9556 (mp) cc_final: 0.9222 (tp) REVERT: Q 155 MET cc_start: 0.8256 (ttp) cc_final: 0.7721 (ttp) REVERT: Q 166 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7619 (ppp) outliers start: 109 outliers final: 67 residues processed: 438 average time/residue: 0.1999 time to fit residues: 142.3538 Evaluate side-chains 407 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 330 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 191 optimal weight: 0.0570 chunk 245 optimal weight: 0.8980 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 283 GLN ** F 589 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 = 0.4059 r_free = 0.4059 target = 0.150526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096726 restraints weight = 55544.862| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.74 r_work: 0.2988 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32308 Z= 0.136 Angle : 0.578 11.940 44112 Z= 0.303 Chirality : 0.043 0.311 5013 Planarity : 0.004 0.061 5355 Dihedral : 16.622 142.547 5426 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.39 % Allowed : 19.77 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.14), residues: 3692 helix: 0.83 (0.13), residues: 1503 sheet: -1.24 (0.24), residues: 404 loop : -1.46 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.014 0.001 TYR F 228 PHE 0.025 0.001 PHE D 176 TRP 0.013 0.001 TRP Q 176 HIS 0.006 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (32296) covalent geometry : angle 0.57534 / 0.30 (44094) hydrogen bonds : bond 0.03841 / 4.31 ( 1445) hydrogen bonds : angle 4.68361 / 5.67 ( 4087) metal coordination : bond 0.00447 / 0.44 ( 12) metal coordination : angle 2.61587 / 2.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 344 time to evaluate : 1.240 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 145 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8584 (tttm) REVERT: B 41 ASN cc_start: 0.8713 (t0) cc_final: 0.8488 (t0) REVERT: B 125 LYS cc_start: 0.9346 (mttm) cc_final: 0.8972 (tttm) REVERT: B 132 HIS cc_start: 0.8696 (m-70) cc_final: 0.8357 (m-70) REVERT: C 299 LYS cc_start: 0.8525 (tptp) cc_final: 0.8046 (tptp) REVERT: C 301 TYR cc_start: 0.8103 (m-10) cc_final: 0.7787 (m-10) REVERT: C 311 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7465 (t) REVERT: C 343 HIS cc_start: 0.8593 (m90) cc_final: 0.8333 (m90) REVERT: C 503 LYS cc_start: 0.8380 (tppt) cc_final: 0.8002 (tptt) REVERT: C 517 GLN cc_start: 0.8628 (pt0) cc_final: 0.8412 (pt0) REVERT: C 546 GLU cc_start: 0.7305 (tt0) cc_final: 0.6028 (mm-30) REVERT: C 693 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9198 (mp) REVERT: C 783 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8776 (mt) REVERT: C 841 ARG cc_start: 0.6510 (mmm160) cc_final: 0.5544 (mtp85) REVERT: C 876 GLU cc_start: 0.7714 (tp30) cc_final: 0.7443 (mm-30) REVERT: C 949 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 996 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7899 (mtm110) REVERT: C 1028 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8999 (mtmm) REVERT: C 1034 ARG cc_start: 0.8845 (tmm-80) cc_final: 0.8616 (ttp80) REVERT: C 1151 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8628 (tt) REVERT: C 1233 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9134 (mt) REVERT: D 129 ASP cc_start: 0.8240 (t0) cc_final: 0.7927 (t70) REVERT: D 151 MET cc_start: 0.7553 (pmm) cc_final: 0.7240 (pmm) REVERT: D 174 ASP cc_start: 0.8218 (m-30) cc_final: 0.7999 (t0) REVERT: D 284 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7708 (p0) REVERT: D 411 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8680 (mm) REVERT: D 504 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: D 698 MET cc_start: 0.8642 (tpt) cc_final: 0.8115 (mmm) REVERT: D 709 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5083 (tpm170) REVERT: D 780 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: D 781 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8139 (ttmm) REVERT: D 1095 MET cc_start: 0.8000 (tmm) cc_final: 0.7500 (tmm) REVERT: D 1189 MET cc_start: 0.8283 (tpt) cc_final: 0.8030 (tpt) REVERT: D 1291 GLU cc_start: 0.8432 (pp20) cc_final: 0.8228 (pp20) REVERT: E 12 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8392 (mmtm) REVERT: F 137 TYR cc_start: 0.7393 (t80) cc_final: 0.6959 (t80) REVERT: F 425 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: F 433 TRP cc_start: 0.8198 (t60) cc_final: 0.7566 (t60) REVERT: Q 56 HIS cc_start: 0.7336 (m90) cc_final: 0.7049 (m170) REVERT: Q 71 MET cc_start: 0.8314 (tpt) cc_final: 0.7960 (tpt) REVERT: Q 96 LEU cc_start: 0.9566 (mp) cc_final: 0.9137 (tp) REVERT: Q 155 MET cc_start: 0.8237 (ttp) cc_final: 0.7644 (ttp) REVERT: Q 166 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7632 (ppp) REVERT: Q 173 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8293 (tm-30) outliers start: 107 outliers final: 71 residues processed: 432 average time/residue: 0.1994 time to fit residues: 139.6488 Evaluate side-chains 414 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 330 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 173 GLN Chi-restraints excluded: chain Q residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 278 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 259 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 157 GLN D 320 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093039 restraints weight = 55158.792| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.58 r_work: 0.2944 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 32308 Z= 0.253 Angle : 0.636 11.515 44112 Z= 0.330 Chirality : 0.046 0.309 5013 Planarity : 0.004 0.065 5355 Dihedral : 16.637 142.500 5421 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.95 % Allowed : 19.68 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.14), residues: 3692 helix: 0.78 (0.13), residues: 1513 sheet: -1.15 (0.25), residues: 402 loop : -1.44 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 33 TYR 0.015 0.001 TYR D 631 PHE 0.025 0.001 PHE C1025 TRP 0.011 0.001 TRP Q 176 HIS 0.008 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (32296) covalent geometry : angle 0.63313 / 0.33 (44094) hydrogen bonds : bond 0.04304 / 4.82 ( 1445) hydrogen bonds : angle 4.74232 / 5.73 ( 4087) metal coordination : bond 0.00837 / 0.75 ( 12) metal coordination : angle 2.94843 / 3.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 335 time to evaluate : 1.180 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 145 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8611 (tttm) REVERT: B 93 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: B 125 LYS cc_start: 0.9336 (mttm) cc_final: 0.8942 (tttm) REVERT: B 132 HIS cc_start: 0.8746 (m-70) cc_final: 0.8357 (m-70) REVERT: B 145 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8153 (tttt) REVERT: C 299 LYS cc_start: 0.8512 (tptp) cc_final: 0.8031 (tptp) REVERT: C 301 TYR cc_start: 0.8140 (m-10) cc_final: 0.7819 (m-10) REVERT: C 311 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7777 (t) REVERT: C 315 MET cc_start: 0.8267 (ptp) cc_final: 0.7959 (ptp) REVERT: C 343 HIS cc_start: 0.8667 (m90) cc_final: 0.8401 (m90) REVERT: C 546 GLU cc_start: 0.7376 (tt0) cc_final: 0.6138 (mm-30) REVERT: C 637 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8586 (ptt180) REVERT: C 693 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9219 (mp) REVERT: C 781 ASP cc_start: 0.8085 (m-30) cc_final: 0.7857 (m-30) REVERT: C 783 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8861 (mt) REVERT: C 841 ARG cc_start: 0.6715 (mmm160) cc_final: 0.5692 (mtp85) REVERT: C 876 GLU cc_start: 0.7701 (tp30) cc_final: 0.7423 (mm-30) REVERT: C 949 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 996 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7858 (mtm110) REVERT: C 1028 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8985 (mtmm) REVERT: C 1034 ARG cc_start: 0.8862 (tmm-80) cc_final: 0.8612 (ttp80) REVERT: C 1233 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9131 (mt) REVERT: D 84 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8653 (mm) REVERT: D 129 ASP cc_start: 0.8215 (t0) cc_final: 0.7921 (t70) REVERT: D 151 MET cc_start: 0.7629 (pmm) cc_final: 0.7325 (pmm) REVERT: D 174 ASP cc_start: 0.8267 (m-30) cc_final: 0.8054 (t0) REVERT: D 196 GLN cc_start: 0.8647 (tp40) cc_final: 0.8346 (tm-30) REVERT: D 284 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7868 (p0) REVERT: D 411 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8693 (mm) REVERT: D 504 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: D 780 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7709 (ttt180) REVERT: E 12 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8411 (mmtm) REVERT: E 53 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8204 (mt-10) REVERT: F 137 TYR cc_start: 0.7307 (t80) cc_final: 0.6945 (t80) REVERT: F 433 TRP cc_start: 0.8231 (t60) cc_final: 0.7610 (t60) REVERT: F 561 MET cc_start: 0.9077 (tpp) cc_final: 0.8671 (mmm) REVERT: Q 53 CYS cc_start: 0.7810 (m) cc_final: 0.7389 (m) REVERT: Q 56 HIS cc_start: 0.7415 (m90) cc_final: 0.7135 (m170) REVERT: Q 96 LEU cc_start: 0.9594 (mp) cc_final: 0.9365 (tp) REVERT: Q 155 MET cc_start: 0.8247 (ttp) cc_final: 0.7712 (ttp) REVERT: Q 166 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7729 (ppp) outliers start: 125 outliers final: 95 residues processed: 436 average time/residue: 0.2003 time to fit residues: 142.5223 Evaluate side-chains 433 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 326 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 173 GLN Chi-restraints excluded: chain Q residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 352 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 376 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 157 GLN D 320 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.4048 r_free = 0.4048 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093756 restraints weight = 55106.781| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.63 r_work: 0.2970 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32308 Z= 0.147 Angle : 0.593 10.789 44112 Z= 0.309 Chirality : 0.044 0.268 5013 Planarity : 0.004 0.063 5355 Dihedral : 16.570 142.877 5421 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.99 % Allowed : 20.06 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.54 (0.14), residues: 3692 helix: 0.95 (0.13), residues: 1501 sheet: -1.09 (0.25), residues: 388 loop : -1.32 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.036 0.001 TYR Q 161 PHE 0.027 0.001 PHE C1025 TRP 0.014 0.001 TRP Q 176 HIS 0.006 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (32296) covalent geometry : angle 0.59109 / 0.31 (44094) hydrogen bonds : bond 0.03896 / 4.37 ( 1445) hydrogen bonds : angle 4.63969 / 5.60 ( 4087) metal coordination : bond 0.00470 / 0.45 ( 12) metal coordination : angle 2.70703 / 2.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 335 time to evaluate : 0.945 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 145 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8775 (tttm) REVERT: B 41 ASN cc_start: 0.8854 (t0) cc_final: 0.8631 (t0) REVERT: B 125 LYS cc_start: 0.9214 (mttm) cc_final: 0.8966 (tttm) REVERT: B 132 HIS cc_start: 0.8751 (m-70) cc_final: 0.8342 (m-70) REVERT: C 299 LYS cc_start: 0.8540 (tptp) cc_final: 0.8071 (tptp) REVERT: C 301 TYR cc_start: 0.8210 (m-10) cc_final: 0.7914 (m-10) REVERT: C 311 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7834 (t) REVERT: C 315 MET cc_start: 0.8401 (ptp) cc_final: 0.8133 (ptp) REVERT: C 343 HIS cc_start: 0.8675 (m90) cc_final: 0.8405 (m90) REVERT: C 503 LYS cc_start: 0.8526 (tppt) cc_final: 0.8124 (tptt) REVERT: C 546 GLU cc_start: 0.7494 (tt0) cc_final: 0.6164 (mm-30) REVERT: C 637 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8570 (ptt180) REVERT: C 693 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9206 (mp) REVERT: C 783 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (mt) REVERT: C 841 ARG cc_start: 0.6660 (mmm160) cc_final: 0.5643 (mtp85) REVERT: C 876 GLU cc_start: 0.7986 (tp30) cc_final: 0.7686 (mm-30) REVERT: C 949 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 996 ARG cc_start: 0.8445 (mtm110) cc_final: 0.7964 (mtm110) REVERT: C 1028 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8978 (mtmm) REVERT: C 1034 ARG cc_start: 0.8890 (tmm-80) cc_final: 0.8647 (ttp80) REVERT: C 1233 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9150 (mt) REVERT: D 84 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8650 (mm) REVERT: D 129 ASP cc_start: 0.8475 (t0) cc_final: 0.8147 (t70) REVERT: D 151 MET cc_start: 0.7678 (pmm) cc_final: 0.7370 (pmm) REVERT: D 174 ASP cc_start: 0.8415 (m-30) cc_final: 0.8118 (t0) REVERT: D 196 GLN cc_start: 0.8745 (tp40) cc_final: 0.8408 (tm-30) REVERT: D 284 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8089 (p0) REVERT: D 411 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8676 (mm) REVERT: D 504 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: D 780 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7864 (ttt180) REVERT: D 1095 MET cc_start: 0.7953 (tmm) cc_final: 0.7403 (tmm) REVERT: D 1189 MET cc_start: 0.8273 (tpt) cc_final: 0.7979 (tpt) REVERT: D 1291 GLU cc_start: 0.8529 (pp20) cc_final: 0.8327 (pp20) REVERT: E 12 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8312 (mmtm) REVERT: F 137 TYR cc_start: 0.7360 (t80) cc_final: 0.6961 (t80) REVERT: F 433 TRP cc_start: 0.8291 (t60) cc_final: 0.7609 (t60) REVERT: F 561 MET cc_start: 0.9110 (tpp) cc_final: 0.8724 (mmm) REVERT: Q 53 CYS cc_start: 0.7854 (m) cc_final: 0.7470 (m) REVERT: Q 71 MET cc_start: 0.8283 (tpt) cc_final: 0.7887 (tpt) REVERT: Q 96 LEU cc_start: 0.9594 (mp) cc_final: 0.9325 (tp) REVERT: Q 155 MET cc_start: 0.8287 (ttp) cc_final: 0.7722 (ttp) REVERT: Q 166 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7721 (ppp) REVERT: Q 173 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8038 (tm-30) outliers start: 126 outliers final: 83 residues processed: 436 average time/residue: 0.2037 time to fit residues: 144.1671 Evaluate side-chains 419 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 325 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 369 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 343 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 157 GLN D 294 ASN D1195 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 283 GLN F 406 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.149924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094423 restraints weight = 55230.777| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.77 r_work: 0.2961 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32308 Z= 0.161 Angle : 0.597 12.583 44112 Z= 0.311 Chirality : 0.044 0.302 5013 Planarity : 0.004 0.063 5355 Dihedral : 16.533 142.908 5421 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.64 % Allowed : 20.82 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.44 (0.14), residues: 3692 helix: 1.01 (0.13), residues: 1503 sheet: -1.00 (0.26), residues: 381 loop : -1.26 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 33 TYR 0.029 0.001 TYR F 430 PHE 0.027 0.001 PHE C1025 TRP 0.008 0.001 TRP D1020 HIS 0.006 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (32296) covalent geometry : angle 0.59447 / 0.31 (44094) hydrogen bonds : bond 0.03912 / 4.39 ( 1445) hydrogen bonds : angle 4.60691 / 5.55 ( 4087) metal coordination : bond 0.00519 / 0.50 ( 12) metal coordination : angle 2.81020 / 2.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 334 time to evaluate : 1.206 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 145 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8605 (tttm) REVERT: B 41 ASN cc_start: 0.8755 (t0) cc_final: 0.8548 (t0) REVERT: B 125 LYS cc_start: 0.9328 (mttm) cc_final: 0.8897 (tttm) REVERT: B 132 HIS cc_start: 0.8736 (m-70) cc_final: 0.8340 (m-70) REVERT: C 299 LYS cc_start: 0.8515 (tptp) cc_final: 0.8041 (tptp) REVERT: C 301 TYR cc_start: 0.8176 (m-10) cc_final: 0.7894 (m-10) REVERT: C 311 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7769 (t) REVERT: C 315 MET cc_start: 0.8383 (ptp) cc_final: 0.8122 (ptp) REVERT: C 343 HIS cc_start: 0.8639 (m90) cc_final: 0.8376 (m90) REVERT: C 503 LYS cc_start: 0.8404 (tppt) cc_final: 0.8003 (tptt) REVERT: C 546 GLU cc_start: 0.7335 (tt0) cc_final: 0.6084 (mm-30) REVERT: C 637 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8597 (ptt180) REVERT: C 693 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9190 (mp) REVERT: C 783 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8776 (mt) REVERT: C 841 ARG cc_start: 0.6623 (mmm160) cc_final: 0.5634 (mtp85) REVERT: C 876 GLU cc_start: 0.7686 (tp30) cc_final: 0.7388 (mm-30) REVERT: C 949 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8434 (tm-30) REVERT: C 996 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7906 (mtm110) REVERT: C 1028 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8979 (mtmm) REVERT: C 1034 ARG cc_start: 0.8861 (tmm-80) cc_final: 0.8640 (ttp80) REVERT: C 1233 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9115 (mt) REVERT: D 84 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 129 ASP cc_start: 0.8254 (t0) cc_final: 0.7942 (t70) REVERT: D 151 MET cc_start: 0.7653 (pmm) cc_final: 0.7369 (pmm) REVERT: D 174 ASP cc_start: 0.8334 (m-30) cc_final: 0.8101 (t0) REVERT: D 196 GLN cc_start: 0.8672 (tp40) cc_final: 0.8351 (tm-30) REVERT: D 284 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7778 (p0) REVERT: D 411 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8683 (mm) REVERT: D 504 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: D 780 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: E 12 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8380 (mmtm) REVERT: F 137 TYR cc_start: 0.7314 (t80) cc_final: 0.6935 (t80) REVERT: F 433 TRP cc_start: 0.8258 (t60) cc_final: 0.7586 (t60) REVERT: F 561 MET cc_start: 0.9099 (tpp) cc_final: 0.8701 (mmm) REVERT: Q 53 CYS cc_start: 0.7893 (m) cc_final: 0.7482 (m) REVERT: Q 71 MET cc_start: 0.8286 (tpt) cc_final: 0.7858 (tpt) REVERT: Q 96 LEU cc_start: 0.9598 (mp) cc_final: 0.9340 (tp) REVERT: Q 155 MET cc_start: 0.8209 (ttp) cc_final: 0.7596 (ttp) REVERT: Q 166 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7699 (ppp) outliers start: 115 outliers final: 87 residues processed: 426 average time/residue: 0.2045 time to fit residues: 141.9915 Evaluate side-chains 420 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 322 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 129 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 280 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 347 optimal weight: 30.0000 chunk 53 optimal weight: 0.0370 chunk 134 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 350 optimal weight: 9.9990 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 157 GLN D1195 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 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 = 0.4055 r_free = 0.4055 target = 0.150345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097068 restraints weight = 54918.948| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.72 r_work: 0.2983 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32308 Z= 0.134 Angle : 0.589 11.698 44112 Z= 0.307 Chirality : 0.043 0.305 5013 Planarity : 0.004 0.062 5355 Dihedral : 16.502 143.053 5420 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.29 % Allowed : 21.16 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.35 (0.14), residues: 3692 helix: 1.07 (0.13), residues: 1504 sheet: -0.85 (0.26), residues: 369 loop : -1.23 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 285 TYR 0.018 0.001 TYR F 430 PHE 0.027 0.001 PHE C1025 TRP 0.053 0.002 TRP Q 176 HIS 0.005 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (32296) covalent geometry : angle 0.58610 / 0.31 (44094) hydrogen bonds : bond 0.03786 / 4.25 ( 1445) hydrogen bonds : angle 4.56149 / 5.49 ( 4087) metal coordination : bond 0.00435 / 0.42 ( 12) metal coordination : angle 2.76867 / 2.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 338 time to evaluate : 1.281 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 145 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8758 (tttm) REVERT: B 41 ASN cc_start: 0.8854 (t0) cc_final: 0.8643 (t0) REVERT: B 125 LYS cc_start: 0.9318 (mttm) cc_final: 0.8891 (tttm) REVERT: B 132 HIS cc_start: 0.8726 (m-70) cc_final: 0.8310 (m-70) REVERT: C 299 LYS cc_start: 0.8517 (tptp) cc_final: 0.8047 (tptp) REVERT: C 301 TYR cc_start: 0.8231 (m-10) cc_final: 0.7931 (m-10) REVERT: C 311 CYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7862 (t) REVERT: C 315 MET cc_start: 0.8387 (ptp) cc_final: 0.8133 (ptp) REVERT: C 343 HIS cc_start: 0.8640 (m90) cc_final: 0.8375 (m90) REVERT: C 503 LYS cc_start: 0.8511 (tppt) cc_final: 0.8110 (tptt) REVERT: C 517 GLN cc_start: 0.8780 (pt0) cc_final: 0.8469 (pt0) REVERT: C 546 GLU cc_start: 0.7471 (tt0) cc_final: 0.6106 (mm-30) REVERT: C 637 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8608 (ptt180) REVERT: C 693 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9223 (mp) REVERT: C 783 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8837 (mt) REVERT: C 841 ARG cc_start: 0.6689 (mmm160) cc_final: 0.5607 (mtp85) REVERT: C 876 GLU cc_start: 0.8011 (tp30) cc_final: 0.7707 (mm-30) REVERT: C 949 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 953 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9009 (mt) REVERT: C 996 ARG cc_start: 0.8461 (mtm110) cc_final: 0.8008 (mtm110) REVERT: C 1028 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8975 (mtmm) REVERT: C 1034 ARG cc_start: 0.8868 (tmm-80) cc_final: 0.8637 (ttp80) REVERT: C 1233 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9151 (mt) REVERT: D 84 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8645 (mm) REVERT: D 129 ASP cc_start: 0.8389 (t0) cc_final: 0.8051 (t70) REVERT: D 151 MET cc_start: 0.7709 (pmm) cc_final: 0.7372 (pmm) REVERT: D 174 ASP cc_start: 0.8426 (m-30) cc_final: 0.8135 (t0) REVERT: D 196 GLN cc_start: 0.8710 (tp40) cc_final: 0.8376 (tm-30) REVERT: D 284 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7992 (p0) REVERT: D 411 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8690 (mm) REVERT: D 504 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: D 780 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: D 1095 MET cc_start: 0.8153 (tmm) cc_final: 0.7605 (tmm) REVERT: D 1189 MET cc_start: 0.8203 (tpt) cc_final: 0.7866 (tpt) REVERT: E 12 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8334 (mmtm) REVERT: F 137 TYR cc_start: 0.7411 (t80) cc_final: 0.7068 (t80) REVERT: F 433 TRP cc_start: 0.8319 (t60) cc_final: 0.7643 (t60) REVERT: Q 49 MET cc_start: 0.7591 (tpp) cc_final: 0.6724 (tpt) REVERT: Q 53 CYS cc_start: 0.7976 (m) cc_final: 0.7576 (m) REVERT: Q 71 MET cc_start: 0.8323 (tpt) cc_final: 0.7973 (tpt) REVERT: Q 96 LEU cc_start: 0.9601 (mp) cc_final: 0.9330 (tp) REVERT: Q 155 MET cc_start: 0.8334 (ttp) cc_final: 0.7735 (ttp) REVERT: Q 166 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7766 (ppp) REVERT: Q 173 GLN cc_start: 0.9239 (mm110) cc_final: 0.8197 (tm-30) outliers start: 104 outliers final: 82 residues processed: 420 average time/residue: 0.2059 time to fit residues: 139.1670 Evaluate side-chains 413 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 319 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1181 ASP Chi-restraints excluded: chain D residue 1195 GLN Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 184 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 285 optimal weight: 50.0000 chunk 308 optimal weight: 0.0170 chunk 229 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 618 GLN D 157 GLN D1195 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093071 restraints weight = 55386.262| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.61 r_work: 0.2947 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32308 Z= 0.252 Angle : 0.650 11.513 44112 Z= 0.336 Chirality : 0.046 0.291 5013 Planarity : 0.004 0.065 5355 Dihedral : 16.547 142.933 5419 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.32 % Allowed : 21.23 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.48 (0.14), residues: 3692 helix: 0.92 (0.13), residues: 1523 sheet: -0.85 (0.26), residues: 378 loop : -1.30 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 33 TYR 0.016 0.001 TYR F 430 PHE 0.027 0.001 PHE C1025 TRP 0.041 0.002 TRP Q 176 HIS 0.006 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (32296) covalent geometry : angle 0.64698 / 0.34 (44094) hydrogen bonds : bond 0.04216 / 4.72 ( 1445) hydrogen bonds : angle 4.65403 / 5.60 ( 4087) metal coordination : bond 0.00830 / 0.74 ( 12) metal coordination : angle 2.95329 / 3.10 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 329 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8789 (tttm) REVERT: B 125 LYS cc_start: 0.9333 (mttm) cc_final: 0.8908 (tttm) REVERT: B 132 HIS cc_start: 0.8776 (m-70) cc_final: 0.8361 (m-70) REVERT: C 238 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: C 299 LYS cc_start: 0.8503 (tptp) cc_final: 0.8022 (tptp) REVERT: C 301 TYR cc_start: 0.8243 (m-10) cc_final: 0.7948 (m-10) REVERT: C 311 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7850 (t) REVERT: C 315 MET cc_start: 0.8410 (ptp) cc_final: 0.8167 (ptp) REVERT: C 343 HIS cc_start: 0.8671 (m90) cc_final: 0.8401 (m90) REVERT: C 546 GLU cc_start: 0.7502 (tt0) cc_final: 0.6103 (mm-30) REVERT: C 637 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8661 (ptt180) REVERT: C 693 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9240 (mp) REVERT: C 783 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8912 (mt) REVERT: C 841 ARG cc_start: 0.6761 (mmm160) cc_final: 0.5705 (mtp85) REVERT: C 876 GLU cc_start: 0.8059 (tp30) cc_final: 0.7741 (mm-30) REVERT: C 949 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8553 (tm-30) REVERT: C 996 ARG cc_start: 0.8431 (mtm110) cc_final: 0.7979 (mtm110) REVERT: C 1028 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8954 (mtmm) REVERT: C 1034 ARG cc_start: 0.8890 (tmm-80) cc_final: 0.8657 (ttp80) REVERT: C 1233 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9144 (mt) REVERT: D 84 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8711 (mm) REVERT: D 129 ASP cc_start: 0.8356 (t0) cc_final: 0.8039 (t70) REVERT: D 151 MET cc_start: 0.7810 (pmm) cc_final: 0.7484 (pmm) REVERT: D 174 ASP cc_start: 0.8497 (m-30) cc_final: 0.8173 (t0) REVERT: D 196 GLN cc_start: 0.8738 (tp40) cc_final: 0.8398 (tm-30) REVERT: D 284 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8095 (p0) REVERT: D 411 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8698 (mm) REVERT: D 504 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: D 780 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7891 (ttt180) REVERT: D 1095 MET cc_start: 0.8045 (tmm) cc_final: 0.7517 (tmm) REVERT: E 12 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8267 (mmtm) REVERT: F 96 ASP cc_start: 0.8253 (t0) cc_final: 0.8035 (t0) REVERT: F 137 TYR cc_start: 0.7502 (t80) cc_final: 0.7091 (t80) REVERT: F 433 TRP cc_start: 0.8361 (t60) cc_final: 0.7667 (t60) REVERT: Q 49 MET cc_start: 0.7426 (tpp) cc_final: 0.6320 (ptt) REVERT: Q 53 CYS cc_start: 0.8030 (m) cc_final: 0.7700 (m) REVERT: Q 71 MET cc_start: 0.8327 (tpt) cc_final: 0.7899 (tpt) REVERT: Q 96 LEU cc_start: 0.9608 (mp) cc_final: 0.9342 (tp) REVERT: Q 155 MET cc_start: 0.8268 (ttp) cc_final: 0.7718 (ttp) REVERT: Q 166 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7743 (ppp) REVERT: Q 173 GLN cc_start: 0.9243 (mm110) cc_final: 0.8194 (tm-30) outliers start: 105 outliers final: 85 residues processed: 415 average time/residue: 0.2031 time to fit residues: 137.5134 Evaluate side-chains 423 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 326 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1181 ASP Chi-restraints excluded: chain D residue 1195 GLN Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 166 MET Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 191 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 157 GLN D1195 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 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 = 0.4049 r_free = 0.4049 target = 0.149945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095319 restraints weight = 55448.381| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.67 r_work: 0.2962 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32308 Z= 0.153 Angle : 0.610 16.749 44112 Z= 0.316 Chirality : 0.044 0.290 5013 Planarity : 0.004 0.066 5355 Dihedral : 16.512 143.132 5417 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.04 % Allowed : 21.61 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.36 (0.14), residues: 3692 helix: 1.04 (0.13), residues: 1510 sheet: -0.87 (0.26), residues: 370 loop : -1.20 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 33 TYR 0.017 0.001 TYR Q 69 PHE 0.028 0.001 PHE C1025 TRP 0.035 0.001 TRP Q 176 HIS 0.005 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (32296) covalent geometry : angle 0.60734 / 0.32 (44094) hydrogen bonds : bond 0.03916 / 4.39 ( 1445) hydrogen bonds : angle 4.61060 / 5.55 ( 4087) metal coordination : bond 0.00508 / 0.48 ( 12) metal coordination : angle 2.85272 / 2.99 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10182.63 seconds wall clock time: 174 minutes 17.75 seconds (10457.75 seconds total)