Starting phenix.real_space_refine on Mon Jul 6 08:51:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a40_15129/07_2026/8a40_15129.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 11 6.06 5 P 85 5.49 5 Mg 3 5.21 5 S 212 5.16 5 C 21260 2.51 5 N 6021 2.21 5 O 6585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34177 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11291 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1356} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 633 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "P" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 302 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "T" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 827 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "U" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1343 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 3, ' ZN': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 118.176 88.558 84.350 1.00107.72 S ATOM 486 SG CYS A 74 118.353 84.838 84.398 1.00105.48 S ATOM 533 SG CYS A 81 114.996 86.524 84.003 1.00100.06 S ATOM 768 SG CYS A 111 101.626 79.898 130.420 1.00144.34 S ATOM 796 SG CYS A 114 105.202 77.680 130.797 1.00146.37 S ATOM 1142 SG CYS A 184 103.453 80.952 132.896 1.00161.55 S ATOM 19923 SG CYS B1119 117.996 72.157 95.216 1.00105.37 S ATOM 19945 SG CYS B1122 115.643 74.492 97.110 1.00104.40 S ATOM 20060 SG CYS B1137 118.831 75.743 95.448 1.00109.04 S ATOM 20081 SG CYS B1140 118.794 73.759 98.760 1.00113.97 S ATOM 28353 SG CYS I 17 42.113 109.383 137.033 1.00122.65 S ATOM 28377 SG CYS I 20 45.649 110.794 136.288 1.00123.48 S ATOM 28538 SG CYS I 39 45.422 107.203 136.970 1.00127.75 S ATOM 28563 SG CYS I 42 44.679 109.609 139.739 1.00129.06 S ATOM 28915 SG CYS I 86 16.248 99.429 101.756 1.00105.91 S ATOM 28939 SG CYS I 89 14.807 102.569 100.301 1.00110.54 S ATOM 29143 SG CYS I 114 18.062 101.086 98.913 1.00 99.22 S ATOM 29178 SG CYS I 119 18.010 102.962 102.155 1.00106.63 S Time building chain proxies: 6.38, per 1000 atoms: 0.19 Number of scatterers: 34177 At special positions: 0 Unit cell: (181.812, 160.128, 170.136, 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 11 29.99 S 212 16.00 P 85 15.00 Mg 3 11.99 O 6585 8.00 N 6021 7.00 C 21260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.06 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 36 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 266 " - pdb=" SG CYS U 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 71 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 184 " pdb=" ZN B1202 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1140 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 119 " Number of angles added : 21 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7654 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 38.7% alpha, 18.4% beta 38 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.514A pdb=" N LYS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.550A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.829A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.632A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.672A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.528A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.558A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.613A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.551A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.817A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.542A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.119A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.276A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.886A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.605A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.542A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.839A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 3.529A pdb=" N ASN A1291 " --> pdb=" O CYS A1287 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 4.010A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.737A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 removed outlier: 3.557A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.509A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 40 through 62 removed outlier: 4.735A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.685A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.703A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 4.456A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.525A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.625A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.881A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.186A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.523A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.534A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.631A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.716A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.847A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.569A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.721A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.066A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.723A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.866A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.915A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.631A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.917A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.654A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.603A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.543A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.558A pdb=" N ILE I 68 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.767A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.604A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.658A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.686A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.124A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'U' and resid 138 through 153 Processing helix chain 'U' and resid 156 through 162 Processing helix chain 'U' and resid 164 through 181 Processing helix chain 'U' and resid 184 through 200 Processing helix chain 'U' and resid 203 through 212 removed outlier: 4.133A pdb=" N ARG U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 222 removed outlier: 3.758A pdb=" N ARG U 222 " --> pdb=" O ASP U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 249 removed outlier: 3.644A pdb=" N ARG U 246 " --> pdb=" O LYS U 242 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU U 247 " --> pdb=" O GLU U 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.621A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 7.093A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.362A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.506A pdb=" N LYS A 331 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.668A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.873A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.400A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.803A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.746A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.553A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.762A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 7.103A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.643A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.643A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.154A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.648A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.575A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.117A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.980A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.980A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.940A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD9, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.645A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.560A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.845A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.561A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.894A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.520A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE8, first strand: chain 'G' and resid 149 through 153 removed outlier: 3.750A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.530A pdb=" N LYS G 129 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.683A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.761A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 271 through 274 removed outlier: 4.047A pdb=" N VAL U 289 " --> pdb=" O TRP U 298 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP U 298 " --> pdb=" O VAL U 289 " (cutoff:3.500A) 1402 hydrogen bonds defined for protein. 3912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 8.64 Time building geometry restraints manager: 3.67 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: 10805 1.34 - 1.46: 7691 1.46 - 1.58: 15982 1.58 - 1.71: 166 1.71 - 1.83: 334 Bond restraints: 34978 Sorted by residual: bond pdb=" C3' DG N 36 " pdb=" C2' DG N 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DC T 16 " pdb=" C2' DC T 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 bond pdb=" C PRO B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.28e-02 6.10e+03 8.66e+00 bond pdb=" C3' DC T 41 " pdb=" C2' DC T 41 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.60e+00 bond pdb=" C3' DC T 33 " pdb=" C2' DC T 33 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.53e+00 ... (remaining 34973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 47066 2.79 - 5.57: 458 5.57 - 8.36: 69 8.36 - 11.15: 11 11.15 - 13.94: 2 Bond angle restraints: 47606 Sorted by residual: angle pdb=" C GLN A 539 " pdb=" CA GLN A 539 " pdb=" CB GLN A 539 " ideal model delta sigma weight residual 116.63 109.35 7.28 1.16e+00 7.43e-01 3.94e+01 angle pdb=" CA GLN A 539 " pdb=" C GLN A 539 " pdb=" N ASP A 540 " ideal model delta sigma weight residual 119.63 115.30 4.33 8.10e-01 1.52e+00 2.85e+01 angle pdb=" N GLU E 96 " pdb=" CA GLU E 96 " pdb=" CB GLU E 96 " ideal model delta sigma weight residual 110.20 118.12 -7.92 1.49e+00 4.50e-01 2.83e+01 angle pdb=" C PRO K 79 " pdb=" N ASP K 80 " pdb=" CA ASP K 80 " ideal model delta sigma weight residual 126.32 135.51 -9.19 1.74e+00 3.30e-01 2.79e+01 angle pdb=" CA MET A1262 " pdb=" CB MET A1262 " pdb=" CG MET A1262 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 ... (remaining 47601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 20629 35.92 - 71.85: 555 71.85 - 107.77: 32 107.77 - 143.69: 0 143.69 - 179.62: 4 Dihedral angle restraints: 21220 sinusoidal: 9391 harmonic: 11829 Sorted by residual: dihedral pdb=" CB CYS L 36 " pdb=" SG CYS L 36 " pdb=" SG CYS L 39 " pdb=" CB CYS L 39 " ideal model delta sinusoidal sigma weight residual 93.00 4.38 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 90 " pdb=" SG CYS C 90 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 -179.04 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS L 19 " pdb=" SG CYS L 19 " pdb=" SG CYS L 39 " pdb=" CB CYS L 39 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 21217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 5049 0.105 - 0.210: 271 0.210 - 0.315: 7 0.315 - 0.419: 0 0.419 - 0.524: 1 Chirality restraints: 5328 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C3' G P 36 " pdb=" C4' G P 36 " pdb=" O3' G P 36 " pdb=" C2' G P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' G P 38 " pdb=" C4' G P 38 " pdb=" O3' G P 38 " pdb=" C2' G P 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5325 not shown) Planarity restraints: 5878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 244 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO A 245 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 252 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LYS U 252 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS U 252 " 0.017 2.00e-02 2.50e+03 pdb=" N THR U 253 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 93 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" CG ASP K 93 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP K 93 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 93 " -0.015 2.00e-02 2.50e+03 ... (remaining 5875 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 457 2.66 - 3.22: 29844 3.22 - 3.78: 53256 3.78 - 4.34: 73482 4.34 - 4.90: 119393 Nonbonded interactions: 276432 Sorted by model distance: nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2006 " model vdw 2.105 2.170 nonbonded pdb=" O ASN B1120 " pdb="ZN ZN B1201 " model vdw 2.121 2.230 nonbonded pdb=" O LEU B1121 " pdb="ZN ZN B1201 " model vdw 2.125 2.230 nonbonded pdb=" O SER I 51 " pdb="ZN ZN A2007 " model vdw 2.127 2.230 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2006 " model vdw 2.135 2.170 ... (remaining 276427 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 : 0.004 0.049 35005 Z= 0.234 Angle : 0.749 13.935 47643 Z= 0.426 Chirality : 0.050 0.524 5328 Planarity : 0.005 0.075 5878 Dihedral : 15.472 179.617 13542 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.65 (0.13), residues: 4022 helix: -0.15 (0.13), residues: 1434 sheet: 0.18 (0.21), residues: 618 loop : -0.76 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 638 TYR 0.040 0.002 TYR B1048 PHE 0.022 0.002 PHE E 73 TRP 0.013 0.002 TRP A1210 HIS 0.008 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.23 (34978) covalent geometry : angle 0.73874 / 0.42 (47606) SS BOND : bond 0.01014 / 0.64 ( 8) SS BOND : angle 5.10724 / 2.86 ( 16) hydrogen bonds : bond 0.18672 / 12.44 ( 1469) hydrogen bonds : angle 6.75993 / 4.85 ( 4108) metal coordination : bond 0.00707 / 0.42 ( 19) metal coordination : angle 4.06566 / 2.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1321 ILE cc_start: 0.9069 (tt) cc_final: 0.8864 (pp) REVERT: B 200 MET cc_start: 0.8208 (tpp) cc_final: 0.7976 (tpt) REVERT: B 262 TYR cc_start: 0.6915 (m-10) cc_final: 0.6704 (m-80) REVERT: F 84 GLU cc_start: 0.8023 (mp0) cc_final: 0.7513 (mp0) REVERT: F 86 GLU cc_start: 0.7397 (mp0) cc_final: 0.6953 (mp0) REVERT: H 37 MET cc_start: 0.8398 (mmt) cc_final: 0.7998 (mmt) REVERT: I 50 ASN cc_start: 0.7946 (t0) cc_final: 0.7731 (t0) REVERT: I 67 GLN cc_start: 0.8707 (mp10) cc_final: 0.8343 (mp10) REVERT: I 99 SER cc_start: 0.9239 (p) cc_final: 0.7956 (p) REVERT: I 122 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8349 (mtm-85) REVERT: K 97 GLU cc_start: 0.7864 (tt0) cc_final: 0.7153 (tt0) REVERT: U 205 ASN cc_start: 0.9253 (p0) cc_final: 0.8755 (p0) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 0.6699 time to fit residues: 318.5159 Evaluate side-chains 310 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain I residue 29 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS A 330 GLN A 341 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN D 66 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 22 ASN I 84 HIS K 113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.058209 restraints weight = 78969.499| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.03 r_work: 0.2688 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35005 Z= 0.232 Angle : 0.644 10.118 47643 Z= 0.339 Chirality : 0.047 0.276 5328 Planarity : 0.005 0.054 5878 Dihedral : 13.734 179.201 5354 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.87 % Allowed : 7.22 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: 0.01 (0.13), residues: 4022 helix: 0.82 (0.14), residues: 1448 sheet: 0.10 (0.20), residues: 642 loop : -0.60 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 33 TYR 0.016 0.001 TYR A1197 PHE 0.031 0.002 PHE U 261 TRP 0.015 0.001 TRP U 298 HIS 0.006 0.001 HIS I 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (34978) covalent geometry : angle 0.63502 / 0.34 (47606) SS BOND : bond 0.01003 / 0.60 ( 8) SS BOND : angle 3.55435 / 2.06 ( 16) hydrogen bonds : bond 0.05145 / 3.38 ( 1469) hydrogen bonds : angle 5.07576 / 3.63 ( 4108) metal coordination : bond 0.00807 / 0.51 ( 19) metal coordination : angle 3.99467 / 2.46 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 335 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.9000 (ttp) cc_final: 0.8746 (ttt) REVERT: A 334 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7311 (ppt-90) REVERT: A 1321 ILE cc_start: 0.9080 (tt) cc_final: 0.8727 (pp) REVERT: B 200 MET cc_start: 0.8937 (tpp) cc_final: 0.8723 (tpt) REVERT: B 494 LYS cc_start: 0.8171 (pttp) cc_final: 0.7791 (mtmm) REVERT: B 733 MET cc_start: 0.8998 (mtp) cc_final: 0.8647 (mtp) REVERT: D 62 MET cc_start: 0.8179 (mmm) cc_final: 0.7853 (mpp) REVERT: E 70 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: E 121 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7283 (tpt) REVERT: F 82 GLU cc_start: 0.7813 (pp20) cc_final: 0.7596 (OUTLIER) REVERT: F 84 GLU cc_start: 0.7990 (mp0) cc_final: 0.7759 (mp0) REVERT: F 86 GLU cc_start: 0.7768 (mp0) cc_final: 0.6971 (mp0) REVERT: I 33 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8237 (mmp-170) REVERT: I 50 ASN cc_start: 0.8227 (t0) cc_final: 0.7997 (t0) REVERT: I 67 GLN cc_start: 0.8985 (mp10) cc_final: 0.8476 (mp10) REVERT: I 99 SER cc_start: 0.8865 (p) cc_final: 0.8582 (p) REVERT: I 122 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8718 (mtm-85) REVERT: K 24 ASP cc_start: 0.8569 (t0) cc_final: 0.8295 (t0) REVERT: L 31 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8392 (ptp90) REVERT: U 236 MET cc_start: 0.9067 (tpp) cc_final: 0.8791 (tpp) outliers start: 31 outliers final: 9 residues processed: 345 average time/residue: 0.6878 time to fit residues: 282.6180 Evaluate side-chains 310 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain U residue 161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 317 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.058843 restraints weight = 78829.866| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.04 r_work: 0.2702 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35005 Z= 0.151 Angle : 0.587 10.326 47643 Z= 0.308 Chirality : 0.045 0.261 5328 Planarity : 0.004 0.048 5878 Dihedral : 13.694 177.970 5347 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.48 % Allowed : 8.84 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: 0.26 (0.13), residues: 4022 helix: 1.16 (0.14), residues: 1442 sheet: 0.08 (0.21), residues: 618 loop : -0.48 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 246 TYR 0.015 0.001 TYR U 158 PHE 0.015 0.001 PHE U 220 TRP 0.014 0.001 TRP B 27 HIS 0.006 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (34978) covalent geometry : angle 0.57843 / 0.31 (47606) SS BOND : bond 0.00934 / 0.49 ( 8) SS BOND : angle 3.64051 / 2.06 ( 16) hydrogen bonds : bond 0.04331 / 2.84 ( 1469) hydrogen bonds : angle 4.73695 / 3.38 ( 4108) metal coordination : bond 0.00642 / 0.39 ( 19) metal coordination : angle 3.75165 / 2.45 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7184 (ppt-90) REVERT: A 520 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9095 (mmt) REVERT: B 200 MET cc_start: 0.8933 (tpp) cc_final: 0.8717 (tpt) REVERT: B 494 LYS cc_start: 0.8202 (pttp) cc_final: 0.7745 (mtmm) REVERT: B 733 MET cc_start: 0.8913 (mtp) cc_final: 0.8597 (mtp) REVERT: D 62 MET cc_start: 0.8315 (mmm) cc_final: 0.8039 (mpp) REVERT: E 70 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: F 84 GLU cc_start: 0.8069 (mp0) cc_final: 0.7619 (mp0) REVERT: H 55 LYS cc_start: 0.9148 (mttp) cc_final: 0.8915 (mttp) REVERT: H 95 LYS cc_start: 0.9283 (ptmt) cc_final: 0.8963 (ptmm) REVERT: I 33 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8298 (mmp-170) REVERT: I 67 GLN cc_start: 0.8937 (mp10) cc_final: 0.8424 (mp10) REVERT: K 97 GLU cc_start: 0.8161 (tt0) cc_final: 0.7942 (tt0) REVERT: L 31 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8401 (ptp90) REVERT: L 35 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8381 (tpp80) REVERT: L 50 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9182 (mmmm) REVERT: U 236 MET cc_start: 0.9114 (tpp) cc_final: 0.8817 (tpp) REVERT: U 250 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7830 (mmp) outliers start: 53 outliers final: 16 residues processed: 347 average time/residue: 0.6737 time to fit residues: 278.8826 Evaluate side-chains 320 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 28 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 376 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 355 optimal weight: 8.9990 chunk 398 optimal weight: 0.2980 chunk 300 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1194 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS C 108 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.058987 restraints weight = 78091.120| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.97 r_work: 0.2708 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35005 Z= 0.141 Angle : 0.566 10.543 47643 Z= 0.295 Chirality : 0.044 0.357 5328 Planarity : 0.004 0.044 5878 Dihedral : 13.709 176.967 5347 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.34 % Allowed : 10.30 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4022 helix: 1.35 (0.14), residues: 1445 sheet: 0.09 (0.21), residues: 616 loop : -0.42 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 122 TYR 0.013 0.001 TYR A 413 PHE 0.014 0.001 PHE E 73 TRP 0.014 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (34978) covalent geometry : angle 0.55759 / 0.29 (47606) SS BOND : bond 0.00701 / 0.40 ( 8) SS BOND : angle 3.03032 / 1.79 ( 16) hydrogen bonds : bond 0.03959 / 2.60 ( 1469) hydrogen bonds : angle 4.55554 / 3.26 ( 4108) metal coordination : bond 0.00598 / 0.36 ( 19) metal coordination : angle 3.74100 / 2.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7296 (ppt-90) REVERT: A 520 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9070 (mmt) REVERT: A 769 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: A 1199 MET cc_start: 0.8404 (pp-130) cc_final: 0.8066 (pp-130) REVERT: A 1262 MET cc_start: 0.8021 (mmm) cc_final: 0.7750 (mmm) REVERT: B 293 GLU cc_start: 0.8968 (mp0) cc_final: 0.8759 (mp0) REVERT: B 733 MET cc_start: 0.8861 (mtp) cc_final: 0.8643 (mtp) REVERT: C 5 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7954 (OUTLIER) REVERT: E 70 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: F 82 GLU cc_start: 0.7692 (pp20) cc_final: 0.7386 (OUTLIER) REVERT: F 84 GLU cc_start: 0.8225 (mp0) cc_final: 0.7890 (mp0) REVERT: F 86 GLU cc_start: 0.7877 (mp0) cc_final: 0.7142 (mp0) REVERT: H 55 LYS cc_start: 0.9130 (mttp) cc_final: 0.8873 (mttp) REVERT: H 95 LYS cc_start: 0.9291 (ptmt) cc_final: 0.8951 (ptmm) REVERT: I 33 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8344 (mmp-170) REVERT: I 67 GLN cc_start: 0.8921 (mp10) cc_final: 0.8408 (mp10) REVERT: I 122 ARG cc_start: 0.9097 (mtm-85) cc_final: 0.8832 (mtm-85) REVERT: K 97 GLU cc_start: 0.8179 (tt0) cc_final: 0.7883 (tt0) REVERT: L 31 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8402 (ptp90) REVERT: L 35 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8307 (tpp80) REVERT: L 56 ASP cc_start: 0.8140 (t0) cc_final: 0.7914 (t0) REVERT: L 58 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8109 (mtt-85) REVERT: U 147 MET cc_start: 0.8834 (mpp) cc_final: 0.8609 (mpp) REVERT: U 189 ASN cc_start: 0.9208 (p0) cc_final: 0.8971 (p0) REVERT: U 236 MET cc_start: 0.9122 (tpp) cc_final: 0.8802 (tpp) REVERT: U 250 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7701 (mpp) outliers start: 48 outliers final: 17 residues processed: 333 average time/residue: 0.6383 time to fit residues: 254.5158 Evaluate side-chains 315 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 187 TYR Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 235 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 373 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 272 optimal weight: 0.0470 chunk 50 optimal weight: 7.9990 chunk 358 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059573 restraints weight = 78753.859| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.02 r_work: 0.2719 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35005 Z= 0.115 Angle : 0.557 10.674 47643 Z= 0.289 Chirality : 0.043 0.304 5328 Planarity : 0.003 0.041 5878 Dihedral : 13.679 176.143 5347 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.43 % Allowed : 11.11 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4022 helix: 1.46 (0.14), residues: 1443 sheet: 0.12 (0.21), residues: 611 loop : -0.36 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 37 TYR 0.017 0.001 TYR G 3 PHE 0.015 0.001 PHE U 220 TRP 0.014 0.001 TRP B 27 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (34978) covalent geometry : angle 0.54800 / 0.29 (47606) SS BOND : bond 0.00961 / 0.51 ( 8) SS BOND : angle 3.66819 / 2.05 ( 16) hydrogen bonds : bond 0.03677 / 2.41 ( 1469) hydrogen bonds : angle 4.42812 / 3.17 ( 4108) metal coordination : bond 0.00526 / 0.30 ( 19) metal coordination : angle 3.45890 / 2.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7141 (ppt-90) REVERT: A 520 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9096 (mmt) REVERT: A 524 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8496 (mmt) REVERT: A 769 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8404 (mtt) REVERT: B 293 GLU cc_start: 0.8955 (mp0) cc_final: 0.8739 (mp0) REVERT: B 733 MET cc_start: 0.8786 (mtp) cc_final: 0.8518 (mtp) REVERT: E 70 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: F 82 GLU cc_start: 0.7737 (pp20) cc_final: 0.7471 (OUTLIER) REVERT: F 83 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8925 (pp) REVERT: F 84 GLU cc_start: 0.8255 (mp0) cc_final: 0.7826 (mp0) REVERT: H 28 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8835 (pp) REVERT: H 55 LYS cc_start: 0.9127 (mttp) cc_final: 0.8866 (mttp) REVERT: H 95 LYS cc_start: 0.9282 (ptmt) cc_final: 0.8927 (ptmm) REVERT: I 33 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8361 (mmp-170) REVERT: I 67 GLN cc_start: 0.8931 (mp10) cc_final: 0.8447 (mp10) REVERT: I 122 ARG cc_start: 0.9117 (mtm-85) cc_final: 0.8807 (mtm-85) REVERT: K 97 GLU cc_start: 0.8193 (tt0) cc_final: 0.7930 (tt0) REVERT: L 31 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (ptp90) REVERT: L 58 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8135 (mtt-85) REVERT: U 158 TYR cc_start: 0.7358 (p90) cc_final: 0.7118 (p90) REVERT: U 189 ASN cc_start: 0.9191 (p0) cc_final: 0.8949 (p0) REVERT: U 236 MET cc_start: 0.9144 (tpp) cc_final: 0.8815 (tpp) REVERT: U 250 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7698 (mpp) outliers start: 51 outliers final: 16 residues processed: 338 average time/residue: 0.6616 time to fit residues: 267.4843 Evaluate side-chains 320 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 135 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 336 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 373 optimal weight: 0.0470 chunk 42 optimal weight: 5.9990 chunk 327 optimal weight: 30.0000 chunk 107 optimal weight: 0.1980 overall best weight: 2.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS C 108 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.058829 restraints weight = 78081.250| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.03 r_work: 0.2707 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35005 Z= 0.140 Angle : 0.563 10.673 47643 Z= 0.291 Chirality : 0.044 0.281 5328 Planarity : 0.003 0.038 5878 Dihedral : 13.673 175.956 5347 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 1.40 % Allowed : 11.84 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 4022 helix: 1.52 (0.14), residues: 1443 sheet: 0.12 (0.21), residues: 610 loop : -0.35 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 35 TYR 0.012 0.001 TYR A 413 PHE 0.015 0.001 PHE C 21 TRP 0.013 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (34978) covalent geometry : angle 0.55610 / 0.29 (47606) SS BOND : bond 0.00648 / 0.36 ( 8) SS BOND : angle 3.10715 / 1.80 ( 16) hydrogen bonds : bond 0.03737 / 2.46 ( 1469) hydrogen bonds : angle 4.38356 / 3.13 ( 4108) metal coordination : bond 0.00552 / 0.34 ( 19) metal coordination : angle 3.37535 / 2.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8332 (p-80) cc_final: 0.7881 (p-80) REVERT: A 334 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7258 (ppt-90) REVERT: A 520 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9067 (mmt) REVERT: A 769 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: A 1262 MET cc_start: 0.7957 (mmm) cc_final: 0.7676 (mmm) REVERT: B 108 MET cc_start: 0.9035 (ttp) cc_final: 0.8640 (ptm) REVERT: B 293 GLU cc_start: 0.8958 (mp0) cc_final: 0.8736 (mp0) REVERT: B 733 MET cc_start: 0.8818 (mtp) cc_final: 0.8485 (mtp) REVERT: B 1132 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9032 (m) REVERT: E 70 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: F 82 GLU cc_start: 0.7800 (pp20) cc_final: 0.7509 (OUTLIER) REVERT: F 84 GLU cc_start: 0.8365 (mp0) cc_final: 0.7975 (mp0) REVERT: F 86 GLU cc_start: 0.7875 (mp0) cc_final: 0.7257 (mp0) REVERT: G 164 MET cc_start: 0.6270 (mpm) cc_final: 0.6039 (tpt) REVERT: H 28 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8828 (pp) REVERT: H 55 LYS cc_start: 0.9138 (mttp) cc_final: 0.8875 (mttp) REVERT: H 95 LYS cc_start: 0.9292 (ptmt) cc_final: 0.8931 (ptmm) REVERT: I 33 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8369 (mmp-170) REVERT: I 67 GLN cc_start: 0.8952 (mp10) cc_final: 0.8440 (mp10) REVERT: J 36 ASP cc_start: 0.8939 (m-30) cc_final: 0.8718 (m-30) REVERT: K 97 GLU cc_start: 0.8207 (tt0) cc_final: 0.7914 (tt0) REVERT: L 31 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (ptp90) REVERT: L 56 ASP cc_start: 0.8083 (t0) cc_final: 0.7871 (t0) REVERT: L 58 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8053 (mtt-85) REVERT: U 147 MET cc_start: 0.9212 (ptp) cc_final: 0.8948 (mpp) REVERT: U 158 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.7247 (p90) REVERT: U 189 ASN cc_start: 0.9209 (p0) cc_final: 0.8991 (p0) REVERT: U 236 MET cc_start: 0.9151 (tpp) cc_final: 0.8826 (tpp) REVERT: U 250 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: U 285 MET cc_start: 0.2042 (ttm) cc_final: 0.1573 (ttp) outliers start: 50 outliers final: 20 residues processed: 329 average time/residue: 0.6376 time to fit residues: 251.9101 Evaluate side-chains 320 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 158 TYR Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 112 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 363 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B1021 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.094939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059445 restraints weight = 78339.834| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.97 r_work: 0.2717 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35005 Z= 0.115 Angle : 0.559 10.657 47643 Z= 0.288 Chirality : 0.043 0.362 5328 Planarity : 0.003 0.038 5878 Dihedral : 13.654 175.469 5347 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 12.40 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 4022 helix: 1.60 (0.14), residues: 1441 sheet: 0.11 (0.21), residues: 610 loop : -0.32 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 122 TYR 0.012 0.001 TYR A 413 PHE 0.016 0.001 PHE G 44 TRP 0.013 0.001 TRP B 27 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (34978) covalent geometry : angle 0.55173 / 0.29 (47606) SS BOND : bond 0.00639 / 0.35 ( 8) SS BOND : angle 2.89139 / 1.70 ( 16) hydrogen bonds : bond 0.03557 / 2.33 ( 1469) hydrogen bonds : angle 4.33276 / 3.09 ( 4108) metal coordination : bond 0.00494 / 0.29 ( 19) metal coordination : angle 3.62601 / 2.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5110 (mmp) REVERT: A 334 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7105 (ppt-90) REVERT: A 520 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9055 (mmt) REVERT: A 769 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8465 (mtt) REVERT: A 1262 MET cc_start: 0.8081 (mmm) cc_final: 0.7751 (mmm) REVERT: A 1292 MET cc_start: 0.7929 (mmp) cc_final: 0.7725 (mtm) REVERT: B 108 MET cc_start: 0.9021 (ttp) cc_final: 0.8632 (ptm) REVERT: B 293 GLU cc_start: 0.8940 (mp0) cc_final: 0.8732 (mp0) REVERT: B 1132 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9029 (m) REVERT: C 164 TYR cc_start: 0.9028 (m-80) cc_final: 0.8791 (m-80) REVERT: E 70 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: F 82 GLU cc_start: 0.7843 (pp20) cc_final: 0.7489 (OUTLIER) REVERT: F 83 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8909 (pp) REVERT: F 84 GLU cc_start: 0.8378 (mp0) cc_final: 0.7896 (mp0) REVERT: G 164 MET cc_start: 0.6325 (mpm) cc_final: 0.6029 (tpt) REVERT: H 28 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8797 (pp) REVERT: H 55 LYS cc_start: 0.9135 (mttp) cc_final: 0.8872 (mttp) REVERT: H 95 LYS cc_start: 0.9288 (ptmt) cc_final: 0.8922 (ptmm) REVERT: I 33 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8399 (mmp-170) REVERT: I 67 GLN cc_start: 0.8933 (mp10) cc_final: 0.8250 (mp10) REVERT: K 97 GLU cc_start: 0.8239 (tt0) cc_final: 0.7934 (tt0) REVERT: L 31 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8493 (ptp90) REVERT: L 56 ASP cc_start: 0.8053 (t0) cc_final: 0.7818 (t0) REVERT: L 58 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8027 (mtt-85) REVERT: U 147 MET cc_start: 0.9186 (ptp) cc_final: 0.8979 (mpp) REVERT: U 158 TYR cc_start: 0.7555 (p90) cc_final: 0.7280 (p90) REVERT: U 159 ILE cc_start: 0.9013 (mp) cc_final: 0.8789 (pp) REVERT: U 189 ASN cc_start: 0.9184 (p0) cc_final: 0.8970 (p0) REVERT: U 236 MET cc_start: 0.9145 (tpp) cc_final: 0.8818 (tpp) REVERT: U 250 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: U 285 MET cc_start: 0.2060 (ttm) cc_final: 0.1619 (ttp) outliers start: 51 outliers final: 22 residues processed: 337 average time/residue: 0.6497 time to fit residues: 262.1987 Evaluate side-chains 324 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 280 optimal weight: 30.0000 chunk 358 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 324 optimal weight: 30.0000 chunk 375 optimal weight: 3.9990 chunk 331 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058457 restraints weight = 78127.401| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.01 r_work: 0.2694 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35005 Z= 0.164 Angle : 0.583 10.685 47643 Z= 0.300 Chirality : 0.044 0.352 5328 Planarity : 0.004 0.043 5878 Dihedral : 13.667 175.694 5347 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 4022 helix: 1.63 (0.14), residues: 1436 sheet: 0.15 (0.21), residues: 611 loop : -0.32 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 122 TYR 0.017 0.001 TYR A 875 PHE 0.015 0.001 PHE C 21 TRP 0.013 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (34978) covalent geometry : angle 0.57524 / 0.30 (47606) SS BOND : bond 0.00663 / 0.36 ( 8) SS BOND : angle 2.85348 / 1.67 ( 16) hydrogen bonds : bond 0.03795 / 2.50 ( 1469) hydrogen bonds : angle 4.35411 / 3.10 ( 4108) metal coordination : bond 0.00567 / 0.35 ( 19) metal coordination : angle 3.75467 / 2.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.5167 (mmp) REVERT: A 301 HIS cc_start: 0.8332 (p-80) cc_final: 0.7859 (p-80) REVERT: A 334 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7311 (ppt-90) REVERT: A 520 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.9029 (mmt) REVERT: A 769 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8563 (mtt) REVERT: A 1428 MET cc_start: 0.8902 (mtp) cc_final: 0.8611 (ttp) REVERT: B 108 MET cc_start: 0.9012 (ttp) cc_final: 0.8636 (ptm) REVERT: B 293 GLU cc_start: 0.8948 (mp0) cc_final: 0.8739 (mp0) REVERT: B 347 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8170 (tpt) REVERT: B 1132 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9046 (m) REVERT: E 70 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: F 82 GLU cc_start: 0.7884 (pp20) cc_final: 0.7576 (OUTLIER) REVERT: F 84 GLU cc_start: 0.8414 (mp0) cc_final: 0.7986 (mp0) REVERT: F 86 GLU cc_start: 0.7875 (mp0) cc_final: 0.7253 (mp0) REVERT: H 28 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8826 (pp) REVERT: H 55 LYS cc_start: 0.9146 (mttp) cc_final: 0.8864 (mttp) REVERT: I 28 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7218 (mm-30) REVERT: I 29 ASP cc_start: 0.7872 (t0) cc_final: 0.6834 (p0) REVERT: I 33 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8369 (mmp-170) REVERT: I 67 GLN cc_start: 0.8944 (mp10) cc_final: 0.8257 (mp10) REVERT: I 82 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7801 (mm-30) REVERT: K 97 GLU cc_start: 0.8291 (tt0) cc_final: 0.8059 (tt0) REVERT: L 31 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8522 (ptp90) REVERT: L 58 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7934 (mtt-85) REVERT: U 147 MET cc_start: 0.9184 (ptp) cc_final: 0.8970 (mpp) REVERT: U 158 TYR cc_start: 0.7643 (p90) cc_final: 0.7400 (p90) REVERT: U 189 ASN cc_start: 0.9202 (p0) cc_final: 0.8980 (p0) REVERT: U 223 MET cc_start: 0.8737 (mmm) cc_final: 0.8129 (mpp) REVERT: U 236 MET cc_start: 0.9153 (tpp) cc_final: 0.8828 (tpp) REVERT: U 250 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: U 285 MET cc_start: 0.2207 (ttm) cc_final: 0.1735 (ttp) outliers start: 50 outliers final: 26 residues processed: 327 average time/residue: 0.6470 time to fit residues: 252.2263 Evaluate side-chains 327 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 187 TYR Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 228 optimal weight: 3.9990 chunk 324 optimal weight: 40.0000 chunk 325 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 369 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058247 restraints weight = 78214.534| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.00 r_work: 0.2689 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35005 Z= 0.168 Angle : 0.599 11.180 47643 Z= 0.309 Chirality : 0.044 0.352 5328 Planarity : 0.004 0.046 5878 Dihedral : 13.678 175.664 5347 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.18 % Allowed : 13.46 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 4022 helix: 1.61 (0.14), residues: 1437 sheet: 0.17 (0.21), residues: 598 loop : -0.32 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 122 TYR 0.016 0.001 TYR U 158 PHE 0.021 0.001 PHE G 44 TRP 0.013 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (34978) covalent geometry : angle 0.59191 / 0.31 (47606) SS BOND : bond 0.00662 / 0.36 ( 8) SS BOND : angle 2.82945 / 1.66 ( 16) hydrogen bonds : bond 0.03852 / 2.55 ( 1469) hydrogen bonds : angle 4.37895 / 3.12 ( 4108) metal coordination : bond 0.00586 / 0.36 ( 19) metal coordination : angle 3.77348 / 2.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5682 (mmt) cc_final: 0.5291 (mmp) REVERT: A 334 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7185 (ppt-90) REVERT: A 388 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (mtp) REVERT: A 520 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9032 (mmt) REVERT: A 769 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8569 (mtt) REVERT: A 1254 LYS cc_start: 0.7484 (tttt) cc_final: 0.7202 (OUTLIER) REVERT: A 1428 MET cc_start: 0.8902 (mtp) cc_final: 0.8574 (ttp) REVERT: B 108 MET cc_start: 0.9006 (ttp) cc_final: 0.8642 (ptm) REVERT: B 293 GLU cc_start: 0.8941 (mp0) cc_final: 0.8730 (mp0) REVERT: B 347 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8199 (tpt) REVERT: B 1132 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9039 (m) REVERT: E 70 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: F 82 GLU cc_start: 0.7941 (pp20) cc_final: 0.7645 (OUTLIER) REVERT: F 84 GLU cc_start: 0.8470 (mp0) cc_final: 0.8020 (mp0) REVERT: F 86 GLU cc_start: 0.7879 (mp0) cc_final: 0.7255 (mp0) REVERT: G 164 MET cc_start: 0.6341 (mpm) cc_final: 0.6054 (tpt) REVERT: H 28 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8821 (pp) REVERT: H 55 LYS cc_start: 0.9136 (mttp) cc_final: 0.8850 (mttp) REVERT: I 28 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7469 (tp30) REVERT: I 29 ASP cc_start: 0.8641 (t0) cc_final: 0.7626 (p0) REVERT: I 33 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8340 (mmp-170) REVERT: I 67 GLN cc_start: 0.8936 (mp10) cc_final: 0.8287 (mp10) REVERT: I 82 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7814 (mm-30) REVERT: L 31 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8539 (ptp90) REVERT: L 56 ASP cc_start: 0.8068 (t0) cc_final: 0.7788 (t0) REVERT: L 58 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8038 (mtt-85) REVERT: U 147 MET cc_start: 0.9198 (ptp) cc_final: 0.8971 (mpp) REVERT: U 189 ASN cc_start: 0.9197 (p0) cc_final: 0.8961 (p0) REVERT: U 223 MET cc_start: 0.8801 (mmm) cc_final: 0.8259 (mpp) REVERT: U 236 MET cc_start: 0.9151 (tpp) cc_final: 0.8826 (tpp) REVERT: U 250 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7717 (mpp) REVERT: U 285 MET cc_start: 0.2093 (ttm) cc_final: 0.1597 (ttp) outliers start: 42 outliers final: 27 residues processed: 325 average time/residue: 0.6586 time to fit residues: 254.9553 Evaluate side-chains 326 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 134 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 291 optimal weight: 50.0000 chunk 368 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** U 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058365 restraints weight = 78079.794| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.99 r_work: 0.2687 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35005 Z= 0.151 Angle : 0.611 14.656 47643 Z= 0.311 Chirality : 0.044 0.347 5328 Planarity : 0.004 0.059 5878 Dihedral : 13.679 175.300 5347 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.01 % Allowed : 13.83 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 4022 helix: 1.61 (0.14), residues: 1437 sheet: 0.17 (0.21), residues: 598 loop : -0.32 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 37 TYR 0.016 0.001 TYR A 875 PHE 0.024 0.001 PHE G 44 TRP 0.013 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (34978) covalent geometry : angle 0.59969 / 0.31 (47606) SS BOND : bond 0.00776 / 0.42 ( 8) SS BOND : angle 4.65255 / 2.49 ( 16) hydrogen bonds : bond 0.03782 / 2.50 ( 1469) hydrogen bonds : angle 4.37661 / 3.11 ( 4108) metal coordination : bond 0.00555 / 0.34 ( 19) metal coordination : angle 3.76162 / 2.32 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5303 (mmp) REVERT: A 334 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7287 (ppt-90) REVERT: A 388 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8719 (mtp) REVERT: A 520 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9023 (mmt) REVERT: A 769 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8557 (mtt) REVERT: A 1254 LYS cc_start: 0.7507 (tttt) cc_final: 0.7226 (mtmt) REVERT: A 1292 MET cc_start: 0.7973 (mmp) cc_final: 0.7767 (mtm) REVERT: A 1428 MET cc_start: 0.8883 (mtp) cc_final: 0.8566 (ttp) REVERT: B 108 MET cc_start: 0.9001 (ttp) cc_final: 0.8652 (ptm) REVERT: B 293 GLU cc_start: 0.8958 (mp0) cc_final: 0.8743 (mp0) REVERT: B 347 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8194 (tpt) REVERT: B 1132 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9040 (m) REVERT: E 70 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: F 82 GLU cc_start: 0.7954 (pp20) cc_final: 0.7640 (OUTLIER) REVERT: F 84 GLU cc_start: 0.8503 (mp0) cc_final: 0.8048 (mp0) REVERT: F 86 GLU cc_start: 0.7851 (mp0) cc_final: 0.7213 (mp0) REVERT: H 28 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8830 (pp) REVERT: H 55 LYS cc_start: 0.9141 (mttp) cc_final: 0.8861 (mttp) REVERT: I 33 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8394 (mtp180) REVERT: I 67 GLN cc_start: 0.8933 (mp10) cc_final: 0.8277 (mp10) REVERT: I 82 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7816 (mm-30) REVERT: L 31 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8565 (ptp90) REVERT: L 56 ASP cc_start: 0.8047 (t0) cc_final: 0.7785 (t0) REVERT: L 58 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8037 (mtt-85) REVERT: U 147 MET cc_start: 0.9208 (ptp) cc_final: 0.8970 (mpp) REVERT: U 189 ASN cc_start: 0.9188 (p0) cc_final: 0.8946 (p0) REVERT: U 223 MET cc_start: 0.8832 (mmm) cc_final: 0.8162 (mpp) REVERT: U 236 MET cc_start: 0.9157 (tpp) cc_final: 0.8833 (tpp) REVERT: U 285 MET cc_start: 0.2113 (ttm) cc_final: 0.1640 (ttp) outliers start: 36 outliers final: 24 residues processed: 320 average time/residue: 0.6886 time to fit residues: 263.2738 Evaluate side-chains 328 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 187 TYR Chi-restraints excluded: chain U residue 250 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 293 optimal weight: 3.9990 chunk 402 optimal weight: 2.9990 chunk 390 optimal weight: 50.0000 chunk 297 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 392 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 274 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS C 108 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.059020 restraints weight = 77751.850| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.01 r_work: 0.2710 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35005 Z= 0.124 Angle : 0.592 13.902 47643 Z= 0.303 Chirality : 0.044 0.341 5328 Planarity : 0.004 0.052 5878 Dihedral : 13.662 174.464 5347 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.90 % Allowed : 13.97 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 4022 helix: 1.65 (0.14), residues: 1436 sheet: 0.13 (0.21), residues: 607 loop : -0.28 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 37 TYR 0.014 0.001 TYR A 875 PHE 0.025 0.001 PHE G 44 TRP 0.012 0.001 TRP B 27 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (34978) covalent geometry : angle 0.58162 / 0.30 (47606) SS BOND : bond 0.00620 / 0.34 ( 8) SS BOND : angle 4.24882 / 2.29 ( 16) hydrogen bonds : bond 0.03578 / 2.36 ( 1469) hydrogen bonds : angle 4.31875 / 3.07 ( 4108) metal coordination : bond 0.00507 / 0.29 ( 19) metal coordination : angle 3.64916 / 2.24 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10479.85 seconds wall clock time: 179 minutes 14.31 seconds (10754.31 seconds total)