Starting phenix.real_space_refine on Tue Sep 15 01:16:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.cif" model { file = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gov_0043/09_2026/6gov_0043.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 116 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 21567 2.51 5 N 6234 2.21 5 O 6990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 35040 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3288 Classifications: {'peptide': 420} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 404} Chain: "B" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1106 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "G" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1377 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 159} Chain breaks: 1 Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 882 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "U" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "V" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "W" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "X" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10410 Classifications: {'peptide': 1339} Link IDs: {'PTRANS': 55, 'TRANS': 1283} Chain breaks: 2 Chain: "K" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 657 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 748 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1029 Classifications: {'RNAv2': 48} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 10, 'rna3p': 37} Chain breaks: 2 Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22658 SG CYS Y 70 113.048 104.962 82.522 1.00159.16 S ATOM 22672 SG CYS Y 72 113.505 104.924 80.503 1.00165.16 S ATOM 22780 SG CYS Y 85 115.289 107.016 81.506 1.00154.68 S ATOM 22804 SG CYS Y 88 111.976 106.062 82.925 1.00160.92 S ATOM 28492 SG CYS Y 814 98.618 98.416 149.340 1.00113.28 S ATOM 29057 SG CYS Y 888 97.093 98.342 146.184 1.00109.86 S ATOM 29108 SG CYS Y 895 98.323 97.059 147.264 1.00 98.95 S ATOM 29129 SG CYS Y 898 96.851 96.699 148.578 1.00 98.91 S Time building chain proxies: 8.74, per 1000 atoms: 0.25 Number of scatterers: 35040 At special positions: 0 Unit cell: (202.5, 172.8, 190.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 130 16.00 P 116 15.00 Mg 1 11.99 O 6990 8.00 N 6234 7.00 C 21567 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: 3.52 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " Number of angles added : 12 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7726 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 53 sheets defined 39.2% alpha, 14.9% beta 35 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.574A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.785A pdb=" N ALA A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 133 removed outlier: 4.460A pdb=" N GLU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.901A pdb=" N LEU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.373A pdb=" N GLY A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.812A pdb=" N ALA A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.805A pdb=" N ALA A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.278A pdb=" N ALA A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 399 through 419 Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.118A pdb=" N ARG B 7 " --> pdb=" O PRO B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.632A pdb=" N GLN B 38 " --> pdb=" O PHE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.563A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 119 through 135 Proline residue: B 132 - end of helix Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 80 through 87 Processing helix chain 'G' and resid 18 through 33 removed outlier: 3.561A pdb=" N VAL G 22 " --> pdb=" O PHE G 18 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA G 23 " --> pdb=" O GLU G 19 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR G 24 " --> pdb=" O GLY G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 114 Processing helix chain 'G' and resid 138 through 142 removed outlier: 3.782A pdb=" N PHE G 141 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 11 Processing helix chain 'N' and resid 11 through 19 removed outlier: 3.656A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.735A pdb=" N ASN N 34 " --> pdb=" O LYS N 31 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 35 " --> pdb=" O PRO N 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 31 through 35' Processing helix chain 'N' and resid 46 through 53 Processing helix chain 'N' and resid 57 through 82 Processing helix chain 'U' and resid 34 through 50 removed outlier: 4.108A pdb=" N THR U 38 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 86 removed outlier: 3.502A pdb=" N ILE U 81 " --> pdb=" O ASP U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 115 No H-bonds generated for 'chain 'U' and resid 113 through 115' Processing helix chain 'U' and resid 154 through 163 removed outlier: 4.035A pdb=" N ARG U 158 " --> pdb=" O PRO U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 233 removed outlier: 4.166A pdb=" N ASP U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 50 removed outlier: 3.878A pdb=" N LEU V 39 " --> pdb=" O PHE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.967A pdb=" N GLY V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 115 No H-bonds generated for 'chain 'V' and resid 113 through 115' Processing helix chain 'V' and resid 212 through 233 removed outlier: 4.090A pdb=" N ALA V 216 " --> pdb=" O ASP V 212 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE V 217 " --> pdb=" O PRO V 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG V 218 " --> pdb=" O GLU V 214 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE V 231 " --> pdb=" O GLN V 227 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP V 233 " --> pdb=" O GLU V 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 32 removed outlier: 3.675A pdb=" N LEU W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 56 removed outlier: 3.537A pdb=" N ILE W 49 " --> pdb=" O LYS W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 91 Processing helix chain 'X' and resid 28 through 39 removed outlier: 3.753A pdb=" N LEU X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 57 removed outlier: 3.602A pdb=" N ALA X 52 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE X 57 " --> pdb=" O PHE X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 206 through 212 Processing helix chain 'X' and resid 216 through 225 Processing helix chain 'X' and resid 242 through 247 Processing helix chain 'X' and resid 270 through 281 Processing helix chain 'X' and resid 288 through 293 Processing helix chain 'X' and resid 318 through 328 Processing helix chain 'X' and resid 346 through 354 removed outlier: 3.559A pdb=" N THR X 350 " --> pdb=" O TYR X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 371 removed outlier: 3.595A pdb=" N ARG X 371 " --> pdb=" O TYR X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 390 removed outlier: 3.868A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 408 Processing helix chain 'X' and resid 421 through 438 removed outlier: 3.690A pdb=" N ILE X 425 " --> pdb=" O SER X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 480 removed outlier: 3.941A pdb=" N MET X 459 " --> pdb=" O SER X 455 " (cutoff:3.500A) Processing helix chain 'X' and resid 495 through 508 removed outlier: 3.815A pdb=" N SER X 499 " --> pdb=" O ALA X 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 528 removed outlier: 3.688A pdb=" N ARG X 528 " --> pdb=" O ILE X 524 " (cutoff:3.500A) Processing helix chain 'X' and resid 609 through 613 removed outlier: 3.535A pdb=" N ASN X 613 " --> pdb=" O GLU X 610 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 674 removed outlier: 3.604A pdb=" N HIS X 673 " --> pdb=" O PHE X 670 " (cutoff:3.500A) Processing helix chain 'X' and resid 675 through 686 Processing helix chain 'X' and resid 687 through 689 No H-bonds generated for 'chain 'X' and resid 687 through 689' Processing helix chain 'X' and resid 704 through 712 Processing helix chain 'X' and resid 738 through 741 removed outlier: 3.703A pdb=" N MET X 741 " --> pdb=" O GLU X 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 738 through 741' Processing helix chain 'X' and resid 820 through 825 Processing helix chain 'X' and resid 859 through 863 Processing helix chain 'X' and resid 898 through 904 Processing helix chain 'X' and resid 942 through 981 removed outlier: 3.906A pdb=" N ASP X 959 " --> pdb=" O GLN X 955 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU X 960 " --> pdb=" O ALA X 956 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA X 969 " --> pdb=" O GLN X 965 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY X 970 " --> pdb=" O ILE X 966 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU X 971 " --> pdb=" O LEU X 967 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA X 981 " --> pdb=" O ALA X 977 " (cutoff:3.500A) Processing helix chain 'X' and resid 985 through 990 Processing helix chain 'X' and resid 993 through 999 Processing helix chain 'X' and resid 1005 through 1038 removed outlier: 3.582A pdb=" N LYS X1035 " --> pdb=" O ALA X1031 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN X1038 " --> pdb=" O ARG X1034 " (cutoff:3.500A) Processing helix chain 'X' and resid 1101 through 1106 removed outlier: 4.093A pdb=" N SER X1105 " --> pdb=" O LEU X1101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG X1106 " --> pdb=" O GLY X1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1101 through 1106' Processing helix chain 'X' and resid 1109 through 1134 removed outlier: 3.896A pdb=" N LEU X1113 " --> pdb=" O ILE X1109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS X1127 " --> pdb=" O GLY X1123 " (cutoff:3.500A) Processing helix chain 'X' and resid 1137 through 1151 removed outlier: 4.012A pdb=" N LEU X1151 " --> pdb=" O ARG X1147 " (cutoff:3.500A) Processing helix chain 'X' and resid 1167 through 1177 Processing helix chain 'X' and resid 1191 through 1202 removed outlier: 3.653A pdb=" N ILE X1195 " --> pdb=" O LYS X1191 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY X1202 " --> pdb=" O LEU X1198 " (cutoff:3.500A) Processing helix chain 'X' and resid 1238 through 1242 Processing helix chain 'X' and resid 1271 through 1281 Processing helix chain 'X' and resid 1284 through 1292 Processing helix chain 'X' and resid 1297 through 1311 Processing helix chain 'X' and resid 1320 through 1331 removed outlier: 3.645A pdb=" N ASN X1324 " --> pdb=" O PRO X1320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 34 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.857A pdb=" N ARG Y 81 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 100 Processing helix chain 'Y' and resid 114 through 119 Processing helix chain 'Y' and resid 122 through 129 Processing helix chain 'Y' and resid 131 through 140 Processing helix chain 'Y' and resid 161 through 172 Processing helix chain 'Y' and resid 181 through 192 removed outlier: 3.578A pdb=" N ILE Y 185 " --> pdb=" O GLY Y 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS Y 190 " --> pdb=" O GLN Y 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET Y 192 " --> pdb=" O LEU Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 207 Processing helix chain 'Y' and resid 210 through 230 Processing helix chain 'Y' and resid 246 through 250 removed outlier: 3.818A pdb=" N ARG Y 250 " --> pdb=" O PRO Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 285 Processing helix chain 'Y' and resid 288 through 308 removed outlier: 3.617A pdb=" N ASP Y 308 " --> pdb=" O ASP Y 304 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 331 removed outlier: 3.537A pdb=" N ILE Y 331 " --> pdb=" O ALA Y 328 " (cutoff:3.500A) Processing helix chain 'Y' and resid 370 through 377 Processing helix chain 'Y' and resid 377 through 388 Processing helix chain 'Y' and resid 393 through 404 removed outlier: 3.808A pdb=" N ALA Y 397 " --> pdb=" O THR Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 417 removed outlier: 4.074A pdb=" N TRP Y 409 " --> pdb=" O GLU Y 405 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP Y 410 " --> pdb=" O ALA Y 406 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG Y 417 " --> pdb=" O ASP Y 413 " (cutoff:3.500A) Processing helix chain 'Y' and resid 453 through 458 Processing helix chain 'Y' and resid 473 through 483 removed outlier: 3.769A pdb=" N GLN Y 477 " --> pdb=" O THR Y 473 " (cutoff:3.500A) Processing helix chain 'Y' and resid 485 through 489 removed outlier: 3.941A pdb=" N ASN Y 489 " --> pdb=" O SER Y 486 " (cutoff:3.500A) Processing helix chain 'Y' and resid 503 through 514 Processing helix chain 'Y' and resid 529 through 539 removed outlier: 3.738A pdb=" N ALA Y 533 " --> pdb=" O GLY Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 574 through 580 Processing helix chain 'Y' and resid 581 through 583 No H-bonds generated for 'chain 'Y' and resid 581 through 583' Processing helix chain 'Y' and resid 588 through 592 Processing helix chain 'Y' and resid 597 through 612 removed outlier: 3.835A pdb=" N ILE Y 601 " --> pdb=" O GLY Y 597 " (cutoff:3.500A) Processing helix chain 'Y' and resid 614 through 636 removed outlier: 3.947A pdb=" N GLY Y 636 " --> pdb=" O ALA Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 640 through 644 removed outlier: 4.055A pdb=" N MET Y 644 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 670 Processing helix chain 'Y' and resid 674 through 703 removed outlier: 4.139A pdb=" N THR Y 703 " --> pdb=" O ASP Y 699 " (cutoff:3.500A) Processing helix chain 'Y' and resid 720 through 728 Processing helix chain 'Y' and resid 733 through 742 removed outlier: 3.613A pdb=" N ILE Y 737 " --> pdb=" O SER Y 733 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Y 741 " --> pdb=" O ILE Y 737 " (cutoff:3.500A) Processing helix chain 'Y' and resid 768 through 804 removed outlier: 4.250A pdb=" N HIS Y 777 " --> pdb=" O PHE Y 773 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY Y 778 " --> pdb=" O ILE Y 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) Processing helix chain 'Y' and resid 805 through 807 No H-bonds generated for 'chain 'Y' and resid 805 through 807' Processing helix chain 'Y' and resid 834 through 839 removed outlier: 3.700A pdb=" N ARG Y 838 " --> pdb=" O PRO Y 834 " (cutoff:3.500A) Processing helix chain 'Y' and resid 865 through 874 Processing helix chain 'Y' and resid 914 through 925 removed outlier: 3.540A pdb=" N ILE Y 918 " --> pdb=" O ALA Y 914 " (cutoff:3.500A) Processing helix chain 'Y' and resid 926 through 930 removed outlier: 3.678A pdb=" N LEU Y 930 " --> pdb=" O GLY Y 927 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1137 through 1146 removed outlier: 3.706A pdb=" N VAL Y1141 " --> pdb=" O GLY Y1137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1216 through 1225 removed outlier: 3.789A pdb=" N ILE Y1220 " --> pdb=" O ALA Y1216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.734A pdb=" N THR Y1230 " --> pdb=" O VAL Y1226 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1259 removed outlier: 4.410A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN Y1259 " --> pdb=" O VAL Y1255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1282 through 1295 removed outlier: 3.597A pdb=" N ASN Y1295 " --> pdb=" O GLU Y1291 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1315 Processing helix chain 'Y' and resid 1327 through 1339 removed outlier: 3.645A pdb=" N VAL Y1331 " --> pdb=" O GLU Y1327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1346 through 1354 removed outlier: 4.025A pdb=" N ASN Y1350 " --> pdb=" O GLY Y1346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1362 through 1375 removed outlier: 3.746A pdb=" N ASP Y1368 " --> pdb=" O ALA Y1364 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG Y1372 " --> pdb=" O ASP Y1368 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA Y1375 " --> pdb=" O ARG Y1371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 145 removed outlier: 4.386A pdb=" N VAL A 141 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 153 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A 145 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 163 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 229 removed outlier: 7.007A pdb=" N ALA A 237 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA A 226 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS A 235 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG A 228 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 233 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA A 234 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 274 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 236 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 299 removed outlier: 3.654A pdb=" N SER A 295 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 8 through 13 Processing sheet with id=AA7, first strand: chain 'G' and resid 46 through 49 Processing sheet with id=AA8, first strand: chain 'G' and resid 167 through 173 removed outlier: 7.347A pdb=" N ARG G 157 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL G 151 " --> pdb=" O ARG G 157 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS G 159 " --> pdb=" O GLU G 149 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN G 145 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 14 through 18 removed outlier: 4.791A pdb=" N ILE U 16 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS U 25 " --> pdb=" O ILE U 16 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP U 199 " --> pdb=" O PRO U 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 97 through 105 removed outlier: 3.797A pdb=" N GLU U 58 " --> pdb=" O LYS U 145 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY U 149 " --> pdb=" O CYS U 54 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS U 54 " --> pdb=" O GLY U 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 90 through 91 Processing sheet with id=AB3, first strand: chain 'U' and resid 108 through 111 removed outlier: 3.859A pdb=" N CYS U 131 " --> pdb=" O VAL U 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 16 through 17 removed outlier: 6.460A pdb=" N ASP V 199 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU V 198 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA V 189 " --> pdb=" O LEU V 198 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS V 200 " --> pdb=" O VAL V 187 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL V 187 " --> pdb=" O LYS V 200 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL V 202 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR V 185 " --> pdb=" O VAL V 202 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU V 204 " --> pdb=" O ILE V 183 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE V 183 " --> pdb=" O GLU V 204 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU V 206 " --> pdb=" O GLU V 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 97 through 105 removed outlier: 3.995A pdb=" N GLU V 58 " --> pdb=" O LYS V 145 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY V 149 " --> pdb=" O CYS V 54 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS V 54 " --> pdb=" O GLY V 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'V' and resid 108 through 111 Processing sheet with id=AB8, first strand: chain 'V' and resid 152 through 153 Processing sheet with id=AB9, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.260A pdb=" N LYS X 13 " --> pdb=" O ALA X1183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.989A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET X 124 " --> pdb=" O LEU X 96 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP X 116 " --> pdb=" O ILE X 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 136 through 137 Processing sheet with id=AC3, first strand: chain 'X' and resid 451 through 454 Processing sheet with id=AC4, first strand: chain 'X' and resid 154 through 158 removed outlier: 3.596A pdb=" N LEU X 184 " --> pdb=" O ILE X 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 284 through 285 removed outlier: 4.032A pdb=" N GLU X 231 " --> pdb=" O GLN X 238 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE X 229 " --> pdb=" O GLU X 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.680A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 296 through 297 removed outlier: 3.635A pdb=" N MET X 315 " --> pdb=" O VAL X 297 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 301 through 302 Processing sheet with id=AC9, first strand: chain 'X' and resid 580 through 581 removed outlier: 5.185A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 580 through 581 Processing sheet with id=AD2, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.541A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 748 through 752 removed outlier: 6.087A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 757 through 758 removed outlier: 3.525A pdb=" N THR X 757 " --> pdb=" O ILE X 765 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 1066 through 1067 removed outlier: 4.294A pdb=" N THR X1226 " --> pdb=" O PHE X 804 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE X 816 " --> pdb=" O SER X1077 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE X1079 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL X 818 " --> pdb=" O ILE X1079 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 1066 through 1067 removed outlier: 3.522A pdb=" N VAL X1225 " --> pdb=" O ILE X1210 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 830 through 841 removed outlier: 6.287A pdb=" N THR X 830 " --> pdb=" O LYS X1057 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS X1057 " --> pdb=" O THR X 830 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS X 832 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA X1055 " --> pdb=" O HIS X 832 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN X 834 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR X1053 " --> pdb=" O GLN X 834 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU X 836 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS X1051 " --> pdb=" O LEU X 836 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS X 838 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE X1049 " --> pdb=" O CYS X 838 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER X 840 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 882 through 884 removed outlier: 6.972A pdb=" N LEU X 918 " --> pdb=" O LEU X 883 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 887 through 889 Processing sheet with id=AE1, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 7.657A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 1268 through 1269 removed outlier: 3.950A pdb=" N GLN X1268 " --> pdb=" O VAL Y 347 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 1335 through 1339 removed outlier: 3.649A pdb=" N LYS Y 21 " --> pdb=" O GLU X1338 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 103 through 112 removed outlier: 10.420A pdb=" N LEU Y 107 " --> pdb=" O PRO Y 243 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N SER Y 109 " --> pdb=" O VAL Y 241 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL Y 241 " --> pdb=" O SER Y 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 145 through 146 removed outlier: 3.524A pdb=" N LYS Y 179 " --> pdb=" O VAL Y 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 316 through 317 removed outlier: 3.712A pdb=" N THR Y 317 " --> pdb=" O ASN Y 320 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN Y 320 " --> pdb=" O THR Y 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Y' and resid 547 through 556 Processing sheet with id=AE8, first strand: chain 'Y' and resid 809 through 811 Processing sheet with id=AE9, first strand: chain 'Y' and resid 820 through 822 Processing sheet with id=AF1, first strand: chain 'Y' and resid 825 through 826 removed outlier: 6.966A pdb=" N VAL Y 825 " --> pdb=" O LYS Y 832 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 957 through 961 removed outlier: 6.530A pdb=" N LEU Y 982 " --> pdb=" O SER Y 994 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER Y 994 " --> pdb=" O LEU Y 982 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU Y 984 " --> pdb=" O LYS Y 992 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AF4, first strand: chain 'Y' and resid 1002 through 1003 Processing sheet with id=AF5, first strand: chain 'Y' and resid 1035 through 1038 Processing sheet with id=AF6, first strand: chain 'Y' and resid 1046 through 1050 Processing sheet with id=AF7, first strand: chain 'Y' and resid 1187 through 1190 removed outlier: 3.836A pdb=" N GLY Y1161 " --> pdb=" O VAL Y1204 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL Y1204 " --> pdb=" O GLY Y1161 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 1280 through 1281 1333 hydrogen bonds defined for protein. 3774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 9.97 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11321 1.34 - 1.46: 7909 1.46 - 1.59: 16122 1.59 - 1.71: 225 1.71 - 1.83: 229 Bond restraints: 35806 Sorted by residual: bond pdb=" C1' DC L 22 " pdb=" N1 DC L 22 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.09e+01 bond pdb=" C1' DC L 24 " pdb=" N1 DC L 24 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" C1' DC L 21 " pdb=" N1 DC L 21 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.89e+01 bond pdb=" C1' DT L 19 " pdb=" N1 DT L 19 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" P DC L 24 " pdb=" O5' DC L 24 " ideal model delta sigma weight residual 1.593 1.631 -0.038 1.00e-02 1.00e+04 1.41e+01 ... (remaining 35801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 47046 2.26 - 4.52: 1607 4.52 - 6.78: 168 6.78 - 9.04: 51 9.04 - 11.30: 10 Bond angle restraints: 48882 Sorted by residual: angle pdb=" O4' DG L 36 " pdb=" C4' DG L 36 " pdb=" C3' DG L 36 " ideal model delta sigma weight residual 106.00 102.20 3.80 6.00e-01 2.78e+00 4.01e+01 angle pdb=" C GLU X 825 " pdb=" N ASP X 826 " pdb=" CA ASP X 826 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" N VAL A 12 " pdb=" CA VAL A 12 " pdb=" C VAL A 12 " ideal model delta sigma weight residual 112.29 107.69 4.60 9.40e-01 1.13e+00 2.40e+01 angle pdb=" CA ARG Y 250 " pdb=" CB ARG Y 250 " pdb=" CG ARG Y 250 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 angle pdb=" C ARG Y 709 " pdb=" N ASP Y 710 " pdb=" CA ASP Y 710 " ideal model delta sigma weight residual 125.66 134.63 -8.97 1.85e+00 2.92e-01 2.35e+01 ... (remaining 48877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.43: 21019 29.43 - 58.85: 692 58.85 - 88.28: 58 88.28 - 117.71: 0 117.71 - 147.14: 2 Dihedral angle restraints: 21771 sinusoidal: 9799 harmonic: 11972 Sorted by residual: dihedral pdb=" C4' C R 59 " pdb=" C3' C R 59 " pdb=" C2' C R 59 " pdb=" C1' C R 59 " ideal model delta sinusoidal sigma weight residual 36.34 -40.46 76.80 1 3.10e+00 1.04e-01 7.71e+02 dihedral pdb=" C4' G R 60 " pdb=" C3' G R 60 " pdb=" C2' G R 60 " pdb=" C1' G R 60 " ideal model delta sinusoidal sigma weight residual 36.34 -40.41 76.75 1 3.10e+00 1.04e-01 7.70e+02 dihedral pdb=" C4' U R 8 " pdb=" C3' U R 8 " pdb=" C2' U R 8 " pdb=" C1' U R 8 " ideal model delta sinusoidal sigma weight residual 36.35 -36.48 72.82 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 21768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 5371 0.129 - 0.257: 221 0.257 - 0.386: 20 0.386 - 0.515: 0 0.515 - 0.643: 1 Chirality restraints: 5613 Sorted by residual: chirality pdb=" CB ILE X1079 " pdb=" CA ILE X1079 " pdb=" CG1 ILE X1079 " pdb=" CG2 ILE X1079 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C2' G R 60 " pdb=" C3' G R 60 " pdb=" O2' G R 60 " pdb=" C1' G R 60 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE Y 754 " pdb=" CA ILE Y 754 " pdb=" CG1 ILE Y 754 " pdb=" CG2 ILE Y 754 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5610 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 120 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO Y 121 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO Y 121 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO Y 121 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Y 438 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.90e+00 pdb=" N PRO Y 439 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Y 439 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 439 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR X1229 " 0.017 2.00e-02 2.50e+03 2.12e-02 9.02e+00 pdb=" CG TYR X1229 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR X1229 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR X1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR X1229 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR X1229 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR X1229 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR X1229 " -0.002 2.00e-02 2.50e+03 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 203 2.55 - 3.14: 25981 3.14 - 3.73: 52671 3.73 - 4.31: 70777 4.31 - 4.90: 115360 Nonbonded interactions: 264992 Sorted by model distance: nonbonded pdb=" N CYS Y 88 " pdb="ZN ZN Y1502 " model vdw 1.963 2.310 nonbonded pdb=" OD1 ASP Y 462 " pdb="MG MG Y1501 " model vdw 1.969 2.170 nonbonded pdb=" OD2 ASP Y 460 " pdb="MG MG Y1501 " model vdw 2.061 2.170 nonbonded pdb=" CB ASP Y 460 " pdb="MG MG Y1501 " model vdw 2.107 2.570 nonbonded pdb=" OE2 GLU A 21 " pdb=" NH1 ARG A 51 " model vdw 2.112 3.120 ... (remaining 264987 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 'U' and (resid 6 through 158 or resid 170 through 234)) selection = (chain 'V' and resid 6 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 44.430 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.008 0.278 35814 Z= 0.374 Angle : 1.164 72.612 48894 Z= 0.557 Chirality : 0.063 0.643 5613 Planarity : 0.007 0.101 5988 Dihedral : 13.366 147.136 14045 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 0.25 % Allowed : 2.69 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.13 % 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: -3.76 (0.11), residues: 4127 helix: -2.26 (0.10), residues: 1446 sheet: -1.73 (0.21), residues: 566 loop : -2.92 (0.11), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 452 TYR 0.047 0.003 TYR X1229 PHE 0.039 0.003 PHE X 812 TRP 0.029 0.003 TRP X 807 HIS 0.008 0.002 HIS Y 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.36 (35806) covalent geometry : angle 0.96008 / 0.54 (48882) hydrogen bonds : bond 0.15171 / 10.30 ( 1421) hydrogen bonds : angle 6.71918 / 4.71 ( 3954) metal coordination : bond 0.17653 / 8.74 ( 8) metal coordination : angle 42.07502 / 22.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 467 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8036 (tt0) cc_final: 0.7805 (pt0) REVERT: A 143 LYS cc_start: 0.6051 (mtmt) cc_final: 0.5801 (mmtt) REVERT: A 147 ARG cc_start: 0.6309 (ptt-90) cc_final: 0.5333 (mmt180) REVERT: A 170 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8840 (mmt180) REVERT: B 46 LEU cc_start: 0.9514 (mt) cc_final: 0.9314 (tp) REVERT: G 18 PHE cc_start: 0.7942 (m-10) cc_final: 0.7672 (m-80) REVERT: G 43 MET cc_start: 0.8243 (ptm) cc_final: 0.7781 (ppp) REVERT: N 1 MET cc_start: 0.0327 (ppp) cc_final: -0.0025 (ppp) REVERT: N 100 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8228 (mmtp) REVERT: U 62 ASP cc_start: 0.7962 (t0) cc_final: 0.7602 (m-30) REVERT: U 95 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8921 (mtmm) REVERT: W 12 LYS cc_start: 0.8651 (tppt) cc_final: 0.8408 (tptt) REVERT: W 56 GLU cc_start: 0.8414 (tt0) cc_final: 0.7842 (tm-30) REVERT: X 11 ILE cc_start: 0.8595 (mm) cc_final: 0.8076 (mm) REVERT: X 105 TYR cc_start: 0.8461 (m-80) cc_final: 0.8158 (m-80) REVERT: X 241 LEU cc_start: 0.8931 (tp) cc_final: 0.8669 (tt) REVERT: X 244 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8932 (tp30) REVERT: X 247 ARG cc_start: 0.9081 (ttm-80) cc_final: 0.8523 (tmm160) REVERT: X 291 TYR cc_start: 0.8757 (t80) cc_final: 0.8407 (t80) REVERT: X 375 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8477 (Cg_endo) REVERT: X 542 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7307 (mtp180) REVERT: X 573 ASN cc_start: 0.8129 (m-40) cc_final: 0.7639 (p0) REVERT: X 653 MET cc_start: 0.9151 (ttt) cc_final: 0.8838 (ttm) REVERT: X 694 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7853 (ttm110) REVERT: X 951 MET cc_start: 0.8483 (ttm) cc_final: 0.8207 (ttm) REVERT: X 1027 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8340 (mttp) REVERT: X 1038 GLN cc_start: 0.9104 (tt0) cc_final: 0.8823 (pp30) REVERT: X 1085 MET cc_start: 0.8796 (mmp) cc_final: 0.8561 (mmp) REVERT: X 1290 MET cc_start: 0.8424 (mmt) cc_final: 0.7835 (mmp) REVERT: Y 47 ARG cc_start: 0.8088 (mmt180) cc_final: 0.7661 (mmp80) REVERT: Y 48 THR cc_start: 0.8907 (p) cc_final: 0.8445 (p) REVERT: Y 66 LYS cc_start: 0.8705 (mttt) cc_final: 0.8374 (mtmm) REVERT: Y 69 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7452 (mm-30) REVERT: Y 90 VAL cc_start: 0.8569 (t) cc_final: 0.7986 (m) REVERT: Y 130 MET cc_start: 0.8823 (ttt) cc_final: 0.8571 (ttp) REVERT: Y 172 PHE cc_start: 0.6953 (m-80) cc_final: 0.6616 (m-10) REVERT: Y 177 ASP cc_start: 0.8941 (t0) cc_final: 0.8566 (t0) REVERT: Y 454 CYS cc_start: 0.8607 (t) cc_final: 0.8398 (t) REVERT: Y 625 MET cc_start: 0.8682 (ttp) cc_final: 0.8390 (ttt) REVERT: Y 651 HIS cc_start: 0.7418 (t70) cc_final: 0.7170 (t-90) REVERT: Y 698 MET cc_start: 0.8912 (tpp) cc_final: 0.8639 (tpp) REVERT: Y 724 MET cc_start: 0.8644 (mtm) cc_final: 0.8428 (mtp) REVERT: Y 785 ASP cc_start: 0.8038 (t0) cc_final: 0.7712 (t0) REVERT: Y 820 ILE cc_start: 0.8492 (pt) cc_final: 0.8253 (mt) REVERT: Y 1189 MET cc_start: 0.8106 (mmm) cc_final: 0.7216 (mmp) outliers start: 9 outliers final: 3 residues processed: 470 average time/residue: 0.2779 time to fit residues: 200.8741 Evaluate side-chains 287 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain Y residue 923 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 133 HIS A 313 ASN B 21 GLN B 105 ASN B 124 ASN E 3 ASN N 15 GLN N 70 ASN V 103 ASN V 132 HIS X 69 GLN X 314 ASN X 343 HIS X1023 HIS ** X1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 HIS Y 164 GLN Y 875 ASN Y1350 ASN Y1366 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110905 restraints weight = 63344.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105875 restraints weight = 48614.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107159 restraints weight = 56440.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107502 restraints weight = 35547.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108927 restraints weight = 30367.578| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35814 Z= 0.194 Angle : 0.857 54.994 48894 Z= 0.390 Chirality : 0.064 1.629 5613 Planarity : 0.006 0.078 5988 Dihedral : 14.913 154.408 5875 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 1.41 % Allowed : 6.98 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.12), residues: 4127 helix: -0.50 (0.12), residues: 1477 sheet: -1.48 (0.21), residues: 536 loop : -2.54 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y1290 TYR 0.038 0.002 TYR X 62 PHE 0.031 0.002 PHE A 24 TRP 0.011 0.001 TRP X 807 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (35806) covalent geometry : angle 0.78324 / 0.39 (48882) hydrogen bonds : bond 0.05394 / 3.55 ( 1421) hydrogen bonds : angle 5.14220 / 3.60 ( 3954) metal coordination : bond 0.01876 / 0.89 ( 8) metal coordination : angle 22.22307 / 12.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6663 (mtmt) cc_final: 0.5737 (mmtt) REVERT: A 147 ARG cc_start: 0.6455 (ptt-90) cc_final: 0.5534 (mmt180) REVERT: A 254 MET cc_start: 0.7546 (mtt) cc_final: 0.6309 (mpp) REVERT: A 305 MET cc_start: -0.4259 (mpp) cc_final: -0.4573 (mpp) REVERT: G 30 ILE cc_start: 0.8937 (mt) cc_final: 0.8022 (mp) REVERT: G 34 ASN cc_start: 0.8744 (t0) cc_final: 0.8456 (t0) REVERT: G 43 MET cc_start: 0.8334 (ptm) cc_final: 0.7903 (ppp) REVERT: G 73 MET cc_start: 0.6939 (mmp) cc_final: 0.6611 (mmm) REVERT: N 100 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8397 (mmtp) REVERT: U 233 ASP cc_start: 0.6881 (t0) cc_final: 0.6535 (t0) REVERT: V 16 ILE cc_start: 0.9154 (mt) cc_final: 0.8910 (tt) REVERT: V 117 HIS cc_start: 0.7240 (t70) cc_final: 0.6645 (t70) REVERT: W 3 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7363 (ttt90) REVERT: W 12 LYS cc_start: 0.8866 (tppt) cc_final: 0.8607 (tptt) REVERT: W 76 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8298 (tm-30) REVERT: X 11 ILE cc_start: 0.8511 (mm) cc_final: 0.8087 (mm) REVERT: X 105 TYR cc_start: 0.7902 (m-80) cc_final: 0.7573 (m-80) REVERT: X 247 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8507 (tmm160) REVERT: X 542 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7295 (mtp85) REVERT: X 653 MET cc_start: 0.8791 (ttt) cc_final: 0.8584 (ttm) REVERT: X 951 MET cc_start: 0.8181 (ttm) cc_final: 0.7978 (ttm) REVERT: X 1064 ASP cc_start: 0.8416 (m-30) cc_final: 0.8059 (m-30) REVERT: X 1085 MET cc_start: 0.8948 (mmp) cc_final: 0.8401 (mmp) REVERT: X 1296 ASP cc_start: 0.8246 (m-30) cc_final: 0.6839 (t0) REVERT: Y 47 ARG cc_start: 0.8133 (mmt180) cc_final: 0.7614 (mmp80) REVERT: Y 66 LYS cc_start: 0.8823 (mttt) cc_final: 0.8573 (mtmm) REVERT: Y 69 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7543 (mm-30) REVERT: Y 90 VAL cc_start: 0.9027 (t) cc_final: 0.8534 (m) REVERT: Y 130 MET cc_start: 0.8374 (ttt) cc_final: 0.8119 (ttp) REVERT: Y 177 ASP cc_start: 0.8728 (t0) cc_final: 0.8512 (t0) REVERT: Y 316 ILE cc_start: 0.8927 (pt) cc_final: 0.8602 (mm) REVERT: Y 625 MET cc_start: 0.8673 (ttp) cc_final: 0.8223 (ttt) REVERT: Y 698 MET cc_start: 0.9121 (tpp) cc_final: 0.8872 (tpp) REVERT: Y 785 ASP cc_start: 0.8060 (t0) cc_final: 0.7738 (t0) REVERT: Y 1040 MET cc_start: 0.6751 (mtm) cc_final: 0.6476 (mtm) REVERT: Y 1189 MET cc_start: 0.8089 (mmm) cc_final: 0.7353 (mmp) outliers start: 50 outliers final: 27 residues processed: 343 average time/residue: 0.2460 time to fit residues: 135.7086 Evaluate side-chains 289 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 240 GLU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 285 LEU Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 923 ILE Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 366 optimal weight: 0.6980 chunk 299 optimal weight: 9.9990 chunk 44 optimal weight: 50.0000 chunk 62 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 385 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN V 66 HIS V 103 ASN X 519 ASN X1312 ASN ** Y1249 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.162339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108790 restraints weight = 63924.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104705 restraints weight = 49562.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105388 restraints weight = 59911.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105609 restraints weight = 37076.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107260 restraints weight = 30316.100| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35814 Z= 0.222 Angle : 0.761 41.290 48894 Z= 0.365 Chirality : 0.051 0.636 5613 Planarity : 0.005 0.076 5988 Dihedral : 14.882 157.386 5875 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.98 % Allowed : 8.11 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 4127 helix: 0.24 (0.13), residues: 1489 sheet: -1.28 (0.22), residues: 541 loop : -2.40 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 88 TYR 0.033 0.002 TYR X1018 PHE 0.028 0.002 PHE A 24 TRP 0.009 0.001 TRP Y 115 HIS 0.006 0.001 HIS X 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (35806) covalent geometry : angle 0.71836 / 0.36 (48882) hydrogen bonds : bond 0.05253 / 3.46 ( 1421) hydrogen bonds : angle 4.87103 / 3.41 ( 3954) metal coordination : bond 0.01869 / 0.88 ( 8) metal coordination : angle 15.98863 / 9.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6718 (mtmt) cc_final: 0.5815 (mmtt) REVERT: A 147 ARG cc_start: 0.6518 (ptt-90) cc_final: 0.5494 (mmt180) REVERT: A 254 MET cc_start: 0.7625 (mtt) cc_final: 0.6359 (mpp) REVERT: A 305 MET cc_start: -0.4141 (mpp) cc_final: -0.4527 (mpp) REVERT: G 18 PHE cc_start: 0.8160 (m-10) cc_final: 0.7915 (m-80) REVERT: G 34 ASN cc_start: 0.8685 (t0) cc_final: 0.8476 (t0) REVERT: G 43 MET cc_start: 0.8345 (ptm) cc_final: 0.7854 (ppp) REVERT: G 73 MET cc_start: 0.6983 (mmp) cc_final: 0.6737 (mmm) REVERT: N 1 MET cc_start: -0.0500 (ppp) cc_final: -0.0808 (ppp) REVERT: N 100 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8376 (mmtp) REVERT: U 8 PHE cc_start: 0.8129 (p90) cc_final: 0.7890 (p90) REVERT: U 233 ASP cc_start: 0.6956 (t0) cc_final: 0.6600 (t0) REVERT: V 16 ILE cc_start: 0.9245 (mt) cc_final: 0.9023 (tt) REVERT: V 117 HIS cc_start: 0.7210 (t70) cc_final: 0.6615 (t70) REVERT: W 12 LYS cc_start: 0.8998 (tppt) cc_final: 0.8721 (tptt) REVERT: W 56 GLU cc_start: 0.8468 (tt0) cc_final: 0.7840 (tm-30) REVERT: W 68 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7487 (tm-30) REVERT: X 11 ILE cc_start: 0.8576 (mm) cc_final: 0.8160 (mm) REVERT: X 105 TYR cc_start: 0.8094 (m-80) cc_final: 0.7792 (m-80) REVERT: X 429 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8083 (mpp) REVERT: X 492 MET cc_start: 0.8263 (ptp) cc_final: 0.7973 (pmm) REVERT: X 542 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7435 (mtt180) REVERT: X 653 MET cc_start: 0.8885 (ttt) cc_final: 0.8680 (ttm) REVERT: X 951 MET cc_start: 0.8257 (ttm) cc_final: 0.8025 (ttm) REVERT: X 1064 ASP cc_start: 0.8427 (m-30) cc_final: 0.8072 (m-30) REVERT: X 1085 MET cc_start: 0.9057 (mmp) cc_final: 0.8539 (mmp) REVERT: X 1180 MET cc_start: 0.8607 (ttt) cc_final: 0.8233 (ttm) REVERT: Y 47 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7674 (mmp80) REVERT: Y 66 LYS cc_start: 0.8811 (mttt) cc_final: 0.8589 (mtmm) REVERT: Y 69 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7768 (mm-30) REVERT: Y 90 VAL cc_start: 0.9102 (t) cc_final: 0.8622 (m) REVERT: Y 130 MET cc_start: 0.8411 (ttt) cc_final: 0.8200 (ttp) REVERT: Y 177 ASP cc_start: 0.8753 (t0) cc_final: 0.8506 (t0) REVERT: Y 316 ILE cc_start: 0.8964 (pt) cc_final: 0.8618 (mm) REVERT: Y 625 MET cc_start: 0.8683 (ttp) cc_final: 0.8182 (ttt) REVERT: Y 651 HIS cc_start: 0.7079 (t70) cc_final: 0.6853 (t-90) REVERT: Y 1040 MET cc_start: 0.6431 (mtm) cc_final: 0.6070 (mtm) REVERT: Y 1189 MET cc_start: 0.8015 (mmm) cc_final: 0.7214 (mmp) outliers start: 70 outliers final: 41 residues processed: 326 average time/residue: 0.2486 time to fit residues: 129.9872 Evaluate side-chains 301 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 240 GLU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 410 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 802 VAL Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain X residue 1337 ILE Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 550 VAL Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain Y residue 923 ILE Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1370 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 67 optimal weight: 20.0000 chunk 416 optimal weight: 50.0000 chunk 42 optimal weight: 50.0000 chunk 249 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 366 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 379 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 HIS N 70 ASN ** Y1249 ASN ** 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 = 0.4176 r_free = 0.4176 target = 0.161446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107985 restraints weight = 63286.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103339 restraints weight = 53905.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104809 restraints weight = 57327.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104797 restraints weight = 39015.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105028 restraints weight = 32929.574| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 35814 Z= 0.244 Angle : 0.732 28.933 48894 Z= 0.361 Chirality : 0.050 0.500 5613 Planarity : 0.005 0.074 5988 Dihedral : 14.816 158.661 5875 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.01 % Allowed : 8.90 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 4127 helix: 0.59 (0.13), residues: 1486 sheet: -1.18 (0.21), residues: 548 loop : -2.32 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 515 TYR 0.031 0.002 TYR X1018 PHE 0.026 0.002 PHE A 24 TRP 0.007 0.001 TRP Y 115 HIS 0.007 0.001 HIS X 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (35806) covalent geometry : angle 0.70763 / 0.36 (48882) hydrogen bonds : bond 0.05264 / 3.44 ( 1421) hydrogen bonds : angle 4.76157 / 3.34 ( 3954) metal coordination : bond 0.01816 / 0.88 ( 8) metal coordination : angle 11.94028 / 6.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6661 (mtmt) cc_final: 0.5735 (mmtt) REVERT: A 147 ARG cc_start: 0.6575 (ptt-90) cc_final: 0.5540 (mmt180) REVERT: A 204 MET cc_start: 0.7077 (tmm) cc_final: 0.6849 (tmm) REVERT: A 305 MET cc_start: -0.3637 (mpp) cc_final: -0.3934 (mpp) REVERT: B 46 LEU cc_start: 0.8818 (tp) cc_final: 0.8392 (pt) REVERT: E 72 ARG cc_start: -0.2589 (mtt180) cc_final: -0.3176 (ptp-170) REVERT: G 34 ASN cc_start: 0.8790 (t0) cc_final: 0.8566 (t0) REVERT: G 43 MET cc_start: 0.8357 (ptm) cc_final: 0.7849 (ppp) REVERT: G 73 MET cc_start: 0.7158 (mmp) cc_final: 0.6434 (mmm) REVERT: N 100 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8486 (mmtp) REVERT: U 233 ASP cc_start: 0.6997 (t0) cc_final: 0.6617 (t0) REVERT: V 117 HIS cc_start: 0.7173 (t70) cc_final: 0.6598 (t70) REVERT: W 3 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7347 (ttt90) REVERT: W 12 LYS cc_start: 0.9035 (tppt) cc_final: 0.8743 (tptt) REVERT: X 5 TYR cc_start: 0.8172 (m-10) cc_final: 0.7961 (m-80) REVERT: X 105 TYR cc_start: 0.7957 (m-80) cc_final: 0.7637 (m-80) REVERT: X 492 MET cc_start: 0.8325 (ptp) cc_final: 0.8120 (pmm) REVERT: X 542 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7390 (mtt180) REVERT: X 731 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8239 (ptt90) REVERT: X 951 MET cc_start: 0.8232 (ttm) cc_final: 0.8007 (ttm) REVERT: X 1064 ASP cc_start: 0.8353 (m-30) cc_final: 0.8046 (m-30) REVERT: X 1085 MET cc_start: 0.9041 (mmp) cc_final: 0.8547 (mmp) REVERT: X 1109 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8798 (tp) REVERT: X 1180 MET cc_start: 0.8643 (ttt) cc_final: 0.8354 (ttp) REVERT: Y 47 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7672 (mmp80) REVERT: Y 66 LYS cc_start: 0.8869 (mttt) cc_final: 0.8565 (mtmm) REVERT: Y 69 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7817 (mt-10) REVERT: Y 90 VAL cc_start: 0.9291 (t) cc_final: 0.8826 (m) REVERT: Y 316 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8717 (mm) REVERT: Y 625 MET cc_start: 0.8700 (ttp) cc_final: 0.8213 (ttt) REVERT: Y 1040 MET cc_start: 0.6627 (mtm) cc_final: 0.6244 (mtm) REVERT: Y 1189 MET cc_start: 0.7969 (mmm) cc_final: 0.7285 (mmp) outliers start: 71 outliers final: 47 residues processed: 311 average time/residue: 0.2502 time to fit residues: 124.8713 Evaluate side-chains 297 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 240 GLU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 410 LEU Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 731 ARG Chi-restraints excluded: chain X residue 764 CYS Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 802 VAL Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain X residue 1292 THR Chi-restraints excluded: chain X residue 1337 ILE Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 550 VAL Chi-restraints excluded: chain Y residue 788 LEU Chi-restraints excluded: chain Y residue 923 ILE Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1370 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 339 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 264 optimal weight: 0.0030 chunk 70 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 349 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 364 optimal weight: 0.0980 chunk 26 optimal weight: 40.0000 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.162524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108463 restraints weight = 63552.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103856 restraints weight = 47601.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104622 restraints weight = 56685.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105469 restraints weight = 35231.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105611 restraints weight = 29591.893| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35814 Z= 0.170 Angle : 0.654 18.287 48894 Z= 0.326 Chirality : 0.047 0.394 5613 Planarity : 0.004 0.071 5988 Dihedral : 14.712 157.476 5875 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.15 % Allowed : 9.67 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4127 helix: 0.91 (0.13), residues: 1486 sheet: -1.10 (0.21), residues: 571 loop : -2.19 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 143 TYR 0.027 0.001 TYR X1018 PHE 0.026 0.001 PHE A 24 TRP 0.007 0.001 TRP Y 115 HIS 0.005 0.001 HIS X 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (35806) covalent geometry : angle 0.64026 / 0.32 (48882) hydrogen bonds : bond 0.04745 / 3.08 ( 1421) hydrogen bonds : angle 4.52569 / 3.17 ( 3954) metal coordination : bond 0.01263 / 0.62 ( 8) metal coordination : angle 8.61195 / 4.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 268 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6734 (mtmt) cc_final: 0.5819 (mmtt) REVERT: A 147 ARG cc_start: 0.6603 (ptt-90) cc_final: 0.5392 (mmt180) REVERT: A 204 MET cc_start: 0.7235 (tmm) cc_final: 0.6833 (tmm) REVERT: B 46 LEU cc_start: 0.8985 (tp) cc_final: 0.8562 (pt) REVERT: E 72 ARG cc_start: -0.2912 (mtt180) cc_final: -0.3267 (ptp-170) REVERT: G 43 MET cc_start: 0.8371 (ptm) cc_final: 0.7782 (ppp) REVERT: G 73 MET cc_start: 0.6989 (mmp) cc_final: 0.6369 (mmm) REVERT: G 90 MET cc_start: 0.6548 (mtp) cc_final: 0.6250 (mtt) REVERT: G 98 ASP cc_start: 0.7609 (t0) cc_final: 0.7220 (t0) REVERT: N 1 MET cc_start: -0.0683 (ppp) cc_final: -0.0926 (ppp) REVERT: N 100 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8508 (mmtp) REVERT: U 8 PHE cc_start: 0.8383 (p90) cc_final: 0.8012 (p90) REVERT: U 231 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7559 (t80) REVERT: U 233 ASP cc_start: 0.6994 (t0) cc_final: 0.6643 (t0) REVERT: V 117 HIS cc_start: 0.7101 (t70) cc_final: 0.6555 (t70) REVERT: W 3 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7338 (ttt90) REVERT: W 12 LYS cc_start: 0.9009 (tppt) cc_final: 0.8733 (tptt) REVERT: X 5 TYR cc_start: 0.8175 (m-10) cc_final: 0.7943 (m-80) REVERT: X 11 ILE cc_start: 0.8511 (mm) cc_final: 0.8165 (mm) REVERT: X 105 TYR cc_start: 0.8096 (m-80) cc_final: 0.7790 (m-80) REVERT: X 247 ARG cc_start: 0.8618 (tmm160) cc_final: 0.8374 (tmm-80) REVERT: X 273 HIS cc_start: 0.9338 (m90) cc_final: 0.9037 (m90) REVERT: X 492 MET cc_start: 0.8358 (ptp) cc_final: 0.8065 (pmm) REVERT: X 542 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7346 (mtt180) REVERT: X 731 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8194 (ptt90) REVERT: X 813 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: X 1018 TYR cc_start: 0.4735 (OUTLIER) cc_final: 0.4070 (p90) REVERT: X 1064 ASP cc_start: 0.8361 (m-30) cc_final: 0.8028 (m-30) REVERT: X 1085 MET cc_start: 0.8984 (mmp) cc_final: 0.8439 (mmp) REVERT: X 1109 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8608 (tp) REVERT: X 1180 MET cc_start: 0.8665 (ttt) cc_final: 0.8307 (ttp) REVERT: X 1296 ASP cc_start: 0.8307 (m-30) cc_final: 0.7161 (t0) REVERT: Y 47 ARG cc_start: 0.8230 (mmt180) cc_final: 0.7664 (mmp80) REVERT: Y 66 LYS cc_start: 0.8898 (mttt) cc_final: 0.8589 (mtmm) REVERT: Y 90 VAL cc_start: 0.9234 (t) cc_final: 0.8623 (m) REVERT: Y 316 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8660 (mm) REVERT: Y 466 MET cc_start: 0.8109 (mtp) cc_final: 0.7675 (ttm) REVERT: Y 707 ILE cc_start: 0.8420 (pt) cc_final: 0.7916 (tt) REVERT: Y 1040 MET cc_start: 0.6588 (mtm) cc_final: 0.6212 (mtm) REVERT: Y 1189 MET cc_start: 0.7940 (mmm) cc_final: 0.7191 (mmp) outliers start: 76 outliers final: 50 residues processed: 329 average time/residue: 0.2421 time to fit residues: 128.6671 Evaluate side-chains 310 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 231 PHE Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 410 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 469 VAL Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 731 ARG Chi-restraints excluded: chain X residue 764 CYS Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 802 VAL Chi-restraints excluded: chain X residue 813 GLU Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 415 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 849 LEU Chi-restraints excluded: chain Y residue 923 ILE Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1370 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 293 optimal weight: 7.9990 chunk 49 optimal weight: 50.0000 chunk 78 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 357 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 46 optimal weight: 50.0000 chunk 208 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 376 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN Y 309 ASN ** Y1249 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.162599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109610 restraints weight = 63394.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104796 restraints weight = 53666.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106328 restraints weight = 57748.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106431 restraints weight = 37674.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107953 restraints weight = 32076.838| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35814 Z= 0.167 Angle : 0.638 11.861 48894 Z= 0.320 Chirality : 0.046 0.363 5613 Planarity : 0.004 0.071 5988 Dihedral : 14.626 157.939 5875 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.26 % Allowed : 10.43 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4127 helix: 1.08 (0.13), residues: 1493 sheet: -1.02 (0.21), residues: 585 loop : -2.07 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 201 TYR 0.026 0.001 TYR X1018 PHE 0.026 0.001 PHE Y 172 TRP 0.007 0.001 TRP Y 115 HIS 0.005 0.001 HIS X 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (35806) covalent geometry : angle 0.63006 / 0.32 (48882) hydrogen bonds : bond 0.04645 / 3.01 ( 1421) hydrogen bonds : angle 4.43952 / 3.11 ( 3954) metal coordination : bond 0.01110 / 0.53 ( 8) metal coordination : angle 6.25629 / 3.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6666 (mtmt) cc_final: 0.5725 (mmtt) REVERT: A 147 ARG cc_start: 0.6652 (ptt-90) cc_final: 0.5467 (mmt180) REVERT: A 166 ASP cc_start: 0.4096 (OUTLIER) cc_final: 0.3715 (p0) REVERT: A 204 MET cc_start: 0.7185 (tmm) cc_final: 0.6890 (tmm) REVERT: B 46 LEU cc_start: 0.8827 (tp) cc_final: 0.8408 (pt) REVERT: E 72 ARG cc_start: -0.2850 (mtt180) cc_final: -0.3169 (ptp-170) REVERT: G 43 MET cc_start: 0.8273 (ptm) cc_final: 0.7758 (ppp) REVERT: G 73 MET cc_start: 0.7144 (mmp) cc_final: 0.6464 (mmm) REVERT: G 90 MET cc_start: 0.6627 (mtp) cc_final: 0.6392 (mtt) REVERT: G 98 ASP cc_start: 0.7555 (t0) cc_final: 0.7168 (t0) REVERT: N 63 TYR cc_start: 0.4617 (OUTLIER) cc_final: 0.4358 (t80) REVERT: N 100 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8442 (mmtp) REVERT: U 231 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7521 (t80) REVERT: U 233 ASP cc_start: 0.6918 (t0) cc_final: 0.6585 (t0) REVERT: V 78 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7384 (tp) REVERT: V 117 HIS cc_start: 0.7112 (t70) cc_final: 0.6645 (t70) REVERT: W 3 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7401 (ttt90) REVERT: W 12 LYS cc_start: 0.9026 (tppt) cc_final: 0.8745 (tptt) REVERT: X 5 TYR cc_start: 0.8114 (m-10) cc_final: 0.7904 (m-80) REVERT: X 105 TYR cc_start: 0.7819 (m-80) cc_final: 0.7480 (m-80) REVERT: X 247 ARG cc_start: 0.8521 (tmm160) cc_final: 0.8220 (tmm-80) REVERT: X 273 HIS cc_start: 0.9226 (m90) cc_final: 0.8886 (m90) REVERT: X 542 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7348 (mtt180) REVERT: X 731 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8253 (ptt90) REVERT: X 1018 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.4020 (p90) REVERT: X 1085 MET cc_start: 0.9011 (mmp) cc_final: 0.8557 (mmp) REVERT: X 1109 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8699 (tp) REVERT: X 1180 MET cc_start: 0.8713 (ttt) cc_final: 0.8404 (ttp) REVERT: X 1296 ASP cc_start: 0.8481 (m-30) cc_final: 0.7274 (t0) REVERT: Y 66 LYS cc_start: 0.8873 (mttt) cc_final: 0.8591 (mtmm) REVERT: Y 69 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7643 (mm-30) REVERT: Y 90 VAL cc_start: 0.9278 (t) cc_final: 0.8695 (m) REVERT: Y 316 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8714 (mm) REVERT: Y 466 MET cc_start: 0.8083 (mtp) cc_final: 0.7715 (ttm) REVERT: Y 707 ILE cc_start: 0.8426 (pt) cc_final: 0.8042 (tt) REVERT: Y 849 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.5734 (mm) REVERT: Y 1040 MET cc_start: 0.6526 (mtm) cc_final: 0.6169 (mtm) REVERT: Y 1189 MET cc_start: 0.7902 (mmm) cc_final: 0.7309 (mmp) outliers start: 80 outliers final: 58 residues processed: 323 average time/residue: 0.2407 time to fit residues: 125.9238 Evaluate side-chains 314 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 231 PHE Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 410 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 469 VAL Chi-restraints excluded: chain X residue 471 VAL Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 635 THR Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 731 ARG Chi-restraints excluded: chain X residue 764 CYS Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 802 VAL Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1082 ILE Chi-restraints excluded: chain X residue 1098 LEU Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 415 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 550 VAL Chi-restraints excluded: chain Y residue 776 THR Chi-restraints excluded: chain Y residue 788 LEU Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 849 LEU Chi-restraints excluded: chain Y residue 853 THR Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1280 VAL Chi-restraints excluded: chain Y residue 1316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 421 optimal weight: 50.0000 chunk 35 optimal weight: 40.0000 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 183 optimal weight: 0.2980 chunk 267 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 259 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN ** Y1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.164170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111189 restraints weight = 63253.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106273 restraints weight = 49504.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107311 restraints weight = 58216.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107982 restraints weight = 35647.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108143 restraints weight = 30141.635| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35814 Z= 0.117 Angle : 0.603 13.522 48894 Z= 0.300 Chirality : 0.045 0.353 5613 Planarity : 0.004 0.069 5988 Dihedral : 14.532 156.719 5873 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.89 % Allowed : 11.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4127 helix: 1.32 (0.14), residues: 1493 sheet: -0.85 (0.22), residues: 579 loop : -1.94 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y1194 TYR 0.025 0.001 TYR X1018 PHE 0.023 0.001 PHE Y 172 TRP 0.008 0.001 TRP N 82 HIS 0.003 0.001 HIS Y 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (35806) covalent geometry : angle 0.59786 / 0.30 (48882) hydrogen bonds : bond 0.04165 / 2.69 ( 1421) hydrogen bonds : angle 4.27472 / 2.99 ( 3954) metal coordination : bond 0.00664 / 0.33 ( 8) metal coordination : angle 4.99580 / 2.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6707 (mtmt) cc_final: 0.5774 (mmtt) REVERT: A 147 ARG cc_start: 0.6650 (ptt-90) cc_final: 0.5486 (mmt180) REVERT: A 166 ASP cc_start: 0.4514 (OUTLIER) cc_final: 0.4013 (p0) REVERT: B 46 LEU cc_start: 0.8894 (tp) cc_final: 0.8474 (pt) REVERT: E 72 ARG cc_start: -0.2905 (mtt180) cc_final: -0.3229 (ptp-170) REVERT: G 43 MET cc_start: 0.8219 (ptm) cc_final: 0.7887 (ppp) REVERT: G 73 MET cc_start: 0.7114 (mmp) cc_final: 0.6487 (mmm) REVERT: G 90 MET cc_start: 0.6811 (mtp) cc_final: 0.6590 (mtt) REVERT: G 98 ASP cc_start: 0.7525 (t0) cc_final: 0.7119 (t0) REVERT: N 63 TYR cc_start: 0.4660 (OUTLIER) cc_final: 0.4372 (t80) REVERT: N 100 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8469 (mmtp) REVERT: U 233 ASP cc_start: 0.6852 (t0) cc_final: 0.6529 (t0) REVERT: V 78 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7304 (tp) REVERT: V 117 HIS cc_start: 0.6959 (t70) cc_final: 0.6552 (t70) REVERT: W 3 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7285 (ttt90) REVERT: W 12 LYS cc_start: 0.8992 (tppt) cc_final: 0.8700 (tptt) REVERT: W 42 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7910 (mp0) REVERT: X 5 TYR cc_start: 0.8075 (m-10) cc_final: 0.7852 (m-80) REVERT: X 11 ILE cc_start: 0.8419 (mm) cc_final: 0.8077 (mm) REVERT: X 105 TYR cc_start: 0.7753 (m-80) cc_final: 0.7495 (m-80) REVERT: X 247 ARG cc_start: 0.8542 (tmm160) cc_final: 0.8269 (tmm-80) REVERT: X 273 HIS cc_start: 0.9255 (m90) cc_final: 0.8912 (m90) REVERT: X 492 MET cc_start: 0.8758 (pmm) cc_final: 0.8484 (pmm) REVERT: X 542 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7253 (mtt180) REVERT: X 731 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8228 (ptt90) REVERT: X 1018 TYR cc_start: 0.4708 (OUTLIER) cc_final: 0.4056 (p90) REVERT: X 1033 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8485 (ppp-140) REVERT: X 1085 MET cc_start: 0.9037 (mmp) cc_final: 0.8620 (mmp) REVERT: X 1109 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8657 (tp) REVERT: X 1180 MET cc_start: 0.8632 (ttt) cc_final: 0.8328 (ttp) REVERT: X 1296 ASP cc_start: 0.8452 (m-30) cc_final: 0.7315 (t0) REVERT: Y 66 LYS cc_start: 0.8899 (mttt) cc_final: 0.8655 (mtmm) REVERT: Y 69 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7620 (mm-30) REVERT: Y 466 MET cc_start: 0.8079 (mtp) cc_final: 0.7817 (ttm) REVERT: Y 707 ILE cc_start: 0.8353 (pt) cc_final: 0.8003 (tt) REVERT: Y 1040 MET cc_start: 0.6149 (mtm) cc_final: 0.5749 (mtm) REVERT: Y 1189 MET cc_start: 0.7871 (mmm) cc_final: 0.7242 (mmp) outliers start: 67 outliers final: 43 residues processed: 333 average time/residue: 0.2505 time to fit residues: 132.5034 Evaluate side-chains 314 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 469 VAL Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 635 THR Chi-restraints excluded: chain X residue 731 ARG Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 800 MET Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1033 ARG Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1082 ILE Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1233 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 788 LEU Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1193 TRP Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 351 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 36 optimal weight: 40.0000 chunk 346 optimal weight: 0.9990 chunk 335 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 93 GLN V 103 ASN ** Y1249 ASN ** 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 = 0.4210 r_free = 0.4210 target = 0.164349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111164 restraints weight = 62912.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106546 restraints weight = 48630.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107418 restraints weight = 58073.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108091 restraints weight = 35976.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108268 restraints weight = 30130.738| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 35814 Z= 0.117 Angle : 0.597 13.237 48894 Z= 0.298 Chirality : 0.044 0.334 5613 Planarity : 0.004 0.069 5988 Dihedral : 14.493 157.146 5873 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.87 % Allowed : 11.36 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % 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: -0.70 (0.13), residues: 4127 helix: 1.41 (0.14), residues: 1495 sheet: -0.76 (0.22), residues: 576 loop : -1.89 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.025 0.001 TYR X1018 PHE 0.026 0.001 PHE Y 172 TRP 0.007 0.001 TRP N 82 HIS 0.003 0.001 HIS Y 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (35806) covalent geometry : angle 0.59337 / 0.30 (48882) hydrogen bonds : bond 0.04074 / 2.63 ( 1421) hydrogen bonds : angle 4.20658 / 2.94 ( 3954) metal coordination : bond 0.00600 / 0.29 ( 8) metal coordination : angle 4.21108 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6740 (mtmt) cc_final: 0.5825 (mmtt) REVERT: A 147 ARG cc_start: 0.6653 (ptt-90) cc_final: 0.5468 (mmt180) REVERT: A 166 ASP cc_start: 0.4334 (OUTLIER) cc_final: 0.3839 (p0) REVERT: A 204 MET cc_start: 0.7173 (tmm) cc_final: 0.6814 (tmm) REVERT: B 46 LEU cc_start: 0.8957 (tp) cc_final: 0.8540 (pt) REVERT: E 72 ARG cc_start: -0.3001 (mtt180) cc_final: -0.3348 (ptp-170) REVERT: G 43 MET cc_start: 0.8077 (ptm) cc_final: 0.7823 (ppp) REVERT: G 73 MET cc_start: 0.7074 (mmp) cc_final: 0.6499 (mmm) REVERT: G 90 MET cc_start: 0.6771 (mtp) cc_final: 0.6564 (mtt) REVERT: N 63 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.4434 (t80) REVERT: N 100 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8476 (mmtp) REVERT: U 233 ASP cc_start: 0.6848 (t0) cc_final: 0.6527 (t0) REVERT: V 78 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (tp) REVERT: V 117 HIS cc_start: 0.6940 (t70) cc_final: 0.6535 (t70) REVERT: W 3 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7265 (ttt90) REVERT: W 11 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7712 (mt-10) REVERT: W 12 LYS cc_start: 0.9004 (tppt) cc_final: 0.8720 (tptt) REVERT: W 42 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7916 (mp0) REVERT: W 56 GLU cc_start: 0.8360 (tt0) cc_final: 0.7723 (tm-30) REVERT: X 11 ILE cc_start: 0.8445 (mm) cc_final: 0.8117 (mm) REVERT: X 105 TYR cc_start: 0.7804 (m-80) cc_final: 0.7562 (m-80) REVERT: X 247 ARG cc_start: 0.8666 (tmm160) cc_final: 0.8339 (tmm-80) REVERT: X 273 HIS cc_start: 0.9281 (m90) cc_final: 0.8936 (m90) REVERT: X 492 MET cc_start: 0.8777 (pmm) cc_final: 0.8563 (pmm) REVERT: X 542 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7218 (mtt180) REVERT: X 1018 TYR cc_start: 0.4759 (OUTLIER) cc_final: 0.4111 (p90) REVERT: X 1033 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8500 (ppp-140) REVERT: X 1085 MET cc_start: 0.9085 (mmp) cc_final: 0.8660 (mmp) REVERT: X 1109 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8625 (tp) REVERT: X 1180 MET cc_start: 0.8630 (ttt) cc_final: 0.8220 (ttp) REVERT: X 1296 ASP cc_start: 0.8477 (m-30) cc_final: 0.7312 (t0) REVERT: Y 66 LYS cc_start: 0.8921 (mttt) cc_final: 0.8661 (mtmm) REVERT: Y 69 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7595 (mm-30) REVERT: Y 466 MET cc_start: 0.8056 (mtp) cc_final: 0.7801 (ttm) REVERT: Y 707 ILE cc_start: 0.8353 (pt) cc_final: 0.8148 (tt) REVERT: Y 849 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.5736 (mm) REVERT: Y 1040 MET cc_start: 0.6039 (mtm) cc_final: 0.5587 (mtm) REVERT: Y 1189 MET cc_start: 0.7861 (mmm) cc_final: 0.7199 (mmp) outliers start: 66 outliers final: 44 residues processed: 328 average time/residue: 0.2545 time to fit residues: 133.5412 Evaluate side-chains 315 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 469 VAL Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 800 MET Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1033 ARG Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1082 ILE Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1233 LEU Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 573 THR Chi-restraints excluded: chain Y residue 788 LEU Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 849 LEU Chi-restraints excluded: chain Y residue 853 THR Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1280 VAL Chi-restraints excluded: chain Y residue 1313 SER Chi-restraints excluded: chain Y residue 1316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 156 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 329 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 19 optimal weight: 40.0000 chunk 362 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN ** Y1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.162969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109295 restraints weight = 63129.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104868 restraints weight = 47121.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105634 restraints weight = 57641.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106561 restraints weight = 34776.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106698 restraints weight = 29039.857| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 35814 Z= 0.167 Angle : 0.625 14.186 48894 Z= 0.313 Chirality : 0.045 0.327 5613 Planarity : 0.004 0.070 5988 Dihedral : 14.485 158.736 5873 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.84 % Allowed : 11.67 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % 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: -0.72 (0.13), residues: 4127 helix: 1.41 (0.14), residues: 1493 sheet: -0.79 (0.21), residues: 595 loop : -1.90 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 281 TYR 0.026 0.001 TYR X1018 PHE 0.026 0.001 PHE Y 172 TRP 0.012 0.001 TRP Y1193 HIS 0.004 0.001 HIS X 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (35806) covalent geometry : angle 0.62265 / 0.31 (48882) hydrogen bonds : bond 0.04372 / 2.83 ( 1421) hydrogen bonds : angle 4.25742 / 2.98 ( 3954) metal coordination : bond 0.00880 / 0.41 ( 8) metal coordination : angle 3.61087 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 259 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.6734 (mtmt) cc_final: 0.5806 (mmtt) REVERT: A 147 ARG cc_start: 0.6811 (ptt-90) cc_final: 0.5462 (mmt180) REVERT: A 166 ASP cc_start: 0.4412 (OUTLIER) cc_final: 0.3939 (p0) REVERT: A 204 MET cc_start: 0.7026 (tmm) cc_final: 0.6647 (tmm) REVERT: B 46 LEU cc_start: 0.8928 (tp) cc_final: 0.8512 (pt) REVERT: E 72 ARG cc_start: -0.2992 (mtt180) cc_final: -0.3321 (ptp-170) REVERT: G 18 PHE cc_start: 0.8236 (m-80) cc_final: 0.8011 (m-80) REVERT: G 43 MET cc_start: 0.8126 (ptm) cc_final: 0.7831 (ppp) REVERT: G 73 MET cc_start: 0.7039 (mmp) cc_final: 0.6492 (mmm) REVERT: G 90 MET cc_start: 0.6798 (mtp) cc_final: 0.6579 (mtt) REVERT: N 100 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8412 (mmtp) REVERT: U 233 ASP cc_start: 0.6672 (t0) cc_final: 0.6322 (t0) REVERT: V 78 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7405 (tp) REVERT: V 117 HIS cc_start: 0.6971 (t70) cc_final: 0.6560 (t70) REVERT: W 3 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7263 (ttt90) REVERT: W 12 LYS cc_start: 0.9004 (tppt) cc_final: 0.8721 (tptt) REVERT: W 42 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7865 (mp0) REVERT: W 56 GLU cc_start: 0.8406 (tt0) cc_final: 0.7721 (tm-30) REVERT: X 105 TYR cc_start: 0.7791 (m-80) cc_final: 0.7546 (m-80) REVERT: X 247 ARG cc_start: 0.8677 (tmm160) cc_final: 0.8344 (tmm-80) REVERT: X 273 HIS cc_start: 0.9278 (m170) cc_final: 0.8925 (m90) REVERT: X 492 MET cc_start: 0.8762 (pmm) cc_final: 0.8536 (pmm) REVERT: X 542 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7444 (mtt180) REVERT: X 1018 TYR cc_start: 0.4782 (OUTLIER) cc_final: 0.4181 (p90) REVERT: X 1033 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8512 (ppp-140) REVERT: X 1085 MET cc_start: 0.9165 (mmp) cc_final: 0.8741 (mmp) REVERT: X 1109 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8739 (tp) REVERT: X 1180 MET cc_start: 0.8652 (ttt) cc_final: 0.8207 (ttp) REVERT: X 1296 ASP cc_start: 0.8601 (m-30) cc_final: 0.7422 (t0) REVERT: Y 66 LYS cc_start: 0.8924 (mttt) cc_final: 0.8366 (mtmm) REVERT: Y 69 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7822 (mt-10) REVERT: Y 466 MET cc_start: 0.8085 (mtp) cc_final: 0.7783 (ttm) REVERT: Y 707 ILE cc_start: 0.8456 (pt) cc_final: 0.8182 (tt) REVERT: Y 849 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.5786 (mm) REVERT: Y 1040 MET cc_start: 0.6064 (mtm) cc_final: 0.5582 (mtm) REVERT: Y 1189 MET cc_start: 0.7842 (mmm) cc_final: 0.7196 (mmp) outliers start: 65 outliers final: 54 residues processed: 309 average time/residue: 0.2412 time to fit residues: 120.5540 Evaluate side-chains 315 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 38 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 183 ILE Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 469 VAL Chi-restraints excluded: chain X residue 471 VAL Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 800 MET Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1033 ARG Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1082 ILE Chi-restraints excluded: chain X residue 1098 LEU Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1233 LEU Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 453 VAL Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 507 VAL Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 550 VAL Chi-restraints excluded: chain Y residue 573 THR Chi-restraints excluded: chain Y residue 788 LEU Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 849 LEU Chi-restraints excluded: chain Y residue 853 THR Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1280 VAL Chi-restraints excluded: chain Y residue 1316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 199 optimal weight: 0.0270 chunk 183 optimal weight: 0.0170 chunk 239 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN ** Y1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.164962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112023 restraints weight = 63136.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107295 restraints weight = 51346.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108985 restraints weight = 51954.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108836 restraints weight = 36759.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109915 restraints weight = 31833.629| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 35814 Z= 0.108 Angle : 0.587 13.490 48894 Z= 0.293 Chirality : 0.044 0.311 5613 Planarity : 0.004 0.068 5988 Dihedral : 14.427 157.225 5873 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.58 % Allowed : 11.98 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % 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: -0.55 (0.13), residues: 4127 helix: 1.53 (0.14), residues: 1497 sheet: -0.58 (0.22), residues: 568 loop : -1.82 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y1194 TYR 0.023 0.001 TYR X1018 PHE 0.029 0.001 PHE Y 172 TRP 0.013 0.001 TRP Y1193 HIS 0.003 0.001 HIS Y 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (35806) covalent geometry : angle 0.58441 / 0.29 (48882) hydrogen bonds : bond 0.03909 / 2.51 ( 1421) hydrogen bonds : angle 4.14410 / 2.90 ( 3954) metal coordination : bond 0.00364 / 0.18 ( 8) metal coordination : angle 3.34821 / 1.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.5799 (mtmt) cc_final: 0.5243 (mmtt) REVERT: A 147 ARG cc_start: 0.6808 (ptt-90) cc_final: 0.5552 (mmt180) REVERT: A 166 ASP cc_start: 0.4608 (OUTLIER) cc_final: 0.3948 (p0) REVERT: A 167 MET cc_start: -0.0349 (tmm) cc_final: -0.0729 (ttp) REVERT: A 204 MET cc_start: 0.7125 (tmm) cc_final: 0.6788 (tmm) REVERT: B 46 LEU cc_start: 0.8865 (tp) cc_final: 0.8449 (pt) REVERT: E 72 ARG cc_start: -0.3101 (mtt180) cc_final: -0.3408 (ptp-170) REVERT: G 18 PHE cc_start: 0.8097 (m-80) cc_final: 0.7830 (m-80) REVERT: G 43 MET cc_start: 0.8091 (ptm) cc_final: 0.7785 (ppp) REVERT: G 73 MET cc_start: 0.7100 (mmp) cc_final: 0.6507 (mmm) REVERT: N 100 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8406 (mmtp) REVERT: U 233 ASP cc_start: 0.6475 (t0) cc_final: 0.6103 (t0) REVERT: V 78 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7176 (tp) REVERT: V 117 HIS cc_start: 0.6821 (t70) cc_final: 0.6483 (t70) REVERT: W 3 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7239 (ttt90) REVERT: W 11 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7619 (mt-10) REVERT: W 12 LYS cc_start: 0.8945 (tppt) cc_final: 0.8643 (tptt) REVERT: W 42 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7881 (mp0) REVERT: W 56 GLU cc_start: 0.8373 (tt0) cc_final: 0.7712 (tm-30) REVERT: X 11 ILE cc_start: 0.8487 (mm) cc_final: 0.8146 (mm) REVERT: X 247 ARG cc_start: 0.8614 (tmm160) cc_final: 0.8271 (tmm-80) REVERT: X 273 HIS cc_start: 0.9224 (m170) cc_final: 0.8867 (m90) REVERT: X 492 MET cc_start: 0.8682 (pmm) cc_final: 0.8472 (pmm) REVERT: X 542 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7395 (mtt180) REVERT: X 1018 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.4117 (p90) REVERT: X 1033 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (ppp-140) REVERT: X 1085 MET cc_start: 0.9054 (mmp) cc_final: 0.8732 (mmp) REVERT: X 1109 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8610 (tp) REVERT: X 1180 MET cc_start: 0.8640 (ttt) cc_final: 0.8269 (ttp) REVERT: X 1296 ASP cc_start: 0.8488 (m-30) cc_final: 0.7347 (t0) REVERT: Y 66 LYS cc_start: 0.8897 (mttt) cc_final: 0.8473 (mtmm) REVERT: Y 466 MET cc_start: 0.8056 (mtp) cc_final: 0.7806 (ttm) REVERT: Y 707 ILE cc_start: 0.8236 (pt) cc_final: 0.8034 (tt) REVERT: Y 849 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.5724 (mm) REVERT: Y 1189 MET cc_start: 0.7827 (mmm) cc_final: 0.7158 (mmp) REVERT: Y 1194 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8288 (ttp80) outliers start: 56 outliers final: 45 residues processed: 320 average time/residue: 0.2425 time to fit residues: 124.4554 Evaluate side-chains 312 residues out of total 3538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain V residue 38 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 47 TYR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 383 SER Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 615 VAL Chi-restraints excluded: chain X residue 630 VAL Chi-restraints excluded: chain X residue 635 THR Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 800 MET Chi-restraints excluded: chain X residue 1018 TYR Chi-restraints excluded: chain X residue 1021 LEU Chi-restraints excluded: chain X residue 1033 ARG Chi-restraints excluded: chain X residue 1077 SER Chi-restraints excluded: chain X residue 1082 ILE Chi-restraints excluded: chain X residue 1109 ILE Chi-restraints excluded: chain X residue 1233 LEU Chi-restraints excluded: chain X residue 1255 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 154 LEU Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 434 ILE Chi-restraints excluded: chain Y residue 442 ILE Chi-restraints excluded: chain Y residue 468 VAL Chi-restraints excluded: chain Y residue 478 LEU Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 573 THR Chi-restraints excluded: chain Y residue 835 LEU Chi-restraints excluded: chain Y residue 849 LEU Chi-restraints excluded: chain Y residue 853 THR Chi-restraints excluded: chain Y residue 1027 VAL Chi-restraints excluded: chain Y residue 1261 LEU Chi-restraints excluded: chain Y residue 1280 VAL Chi-restraints excluded: chain Y residue 1313 SER Chi-restraints excluded: chain Y residue 1316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 142 optimal weight: 0.8980 chunk 363 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 177 optimal weight: 0.3980 chunk 282 optimal weight: 5.9990 chunk 339 optimal weight: 0.9990 chunk 348 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 385 optimal weight: 40.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 103 ASN ** X1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.165622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112796 restraints weight = 62772.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108707 restraints weight = 47821.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109539 restraints weight = 56702.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110531 restraints weight = 34383.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111871 restraints weight = 28733.032| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 35814 Z= 0.104 Angle : 0.581 14.432 48894 Z= 0.290 Chirality : 0.044 0.303 5613 Planarity : 0.004 0.067 5988 Dihedral : 14.375 157.605 5873 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.44 % Allowed : 12.35 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % 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: -0.43 (0.13), residues: 4127 helix: 1.61 (0.14), residues: 1499 sheet: -0.55 (0.22), residues: 568 loop : -1.72 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 33 TYR 0.028 0.001 TYR U 185 PHE 0.031 0.001 PHE Y 172 TRP 0.014 0.001 TRP Y1193 HIS 0.003 0.000 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (35806) covalent geometry : angle 0.57948 / 0.29 (48882) hydrogen bonds : bond 0.03782 / 2.43 ( 1421) hydrogen bonds : angle 4.08037 / 2.85 ( 3954) metal coordination : bond 0.00335 / 0.16 ( 8) metal coordination : angle 2.85516 / 1.59 ( 12) =============================================================================== Job complete usr+sys time: 6012.21 seconds wall clock time: 104 minutes 43.77 seconds (6283.77 seconds total)