Starting phenix.real_space_refine on Sun Jun 29 08:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_15129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_15129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_15129.map" model { file = "/net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_15129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a40_15129/06_2025/8a40_15129.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'ASN:plan1': 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: {'GLN:plan1': 3, 'GLU:plan': 5, '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: {'GLU:plan': 1, 'ASN:plan1': 2, '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: 19.27, per 1000 atoms: 0.56 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: 8.85 Conformation dependent library (CDL) restraints added in 4.4 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: 13.08 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: 19.51 Time building geometry restraints manager: 10.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 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=" 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=" CA GLU I 105 " pdb=" CB GLU I 105 " ideal model delta sigma weight residual 1.517 1.564 -0.047 2.41e-02 1.72e+03 3.86e+00 bond pdb=" C3' G P 36 " pdb=" O3' G P 36 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 3.08e+00 bond pdb=" C ARG H 81 " pdb=" N PRO H 82 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 bond pdb=" CA THR A 832 " pdb=" C THR A 832 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.87e+00 ... (remaining 34973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 47068 2.79 - 5.57: 456 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: 20645 35.92 - 71.85: 579 71.85 - 107.77: 36 107.77 - 143.69: 0 143.69 - 179.62: 4 Dihedral angle restraints: 21264 sinusoidal: 9435 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 21261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 5054 0.105 - 0.210: 266 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 98.030 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.140 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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= 0.187 Angle : 0.735 13.935 47643 Z= 0.393 Chirality : 0.050 0.524 5328 Planarity : 0.005 0.075 5878 Dihedral : 15.666 179.617 13586 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP A1210 HIS 0.008 0.001 HIS A 804 PHE 0.022 0.002 PHE E 73 TYR 0.040 0.002 TYR B1048 ARG 0.021 0.001 ARG B 638 Details of bonding type rmsd hydrogen bonds : bond 0.18672 ( 1469) hydrogen bonds : angle 6.75993 ( 4108) metal coordination : bond 0.00707 ( 19) metal coordination : angle 4.06566 ( 21) SS BOND : bond 0.01014 ( 8) SS BOND : angle 5.10724 ( 16) covalent geometry : bond 0.00417 (34978) covalent geometry : angle 0.72477 (47606) *********************** 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 : 3.661 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: 1.5468 time to fit residues: 736.9929 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 : 3.955 ------------------------------------------------------------------------------- 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 344 optimal weight: 10.0000 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 9.9990 overall best weight: 5.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 330 GLN A 341 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1251 ASN ** 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** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN D 66 ASN F 46 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.092845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.057059 restraints weight = 78492.041| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.01 r_work: 0.2662 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 35005 Z= 0.281 Angle : 0.664 10.679 47643 Z= 0.347 Chirality : 0.047 0.270 5328 Planarity : 0.005 0.060 5878 Dihedral : 14.197 179.667 5398 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.01 % Allowed : 7.53 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4022 helix: 0.82 (0.14), residues: 1450 sheet: 0.13 (0.21), residues: 627 loop : -0.57 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 298 HIS 0.007 0.001 HIS I 84 PHE 0.017 0.002 PHE C 63 TYR 0.018 0.002 TYR B 752 ARG 0.008 0.001 ARG B 638 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 1469) hydrogen bonds : angle 4.99637 ( 4108) metal coordination : bond 0.00928 ( 19) metal coordination : angle 4.42095 ( 21) SS BOND : bond 0.01095 ( 8) SS BOND : angle 3.24027 ( 16) covalent geometry : bond 0.00652 (34978) covalent geometry : angle 0.65459 (47606) *********************** 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 374 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.9026 (ttp) cc_final: 0.8745 (ttt) REVERT: A 334 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7271 (ppt-90) REVERT: A 1321 ILE cc_start: 0.9095 (tt) cc_final: 0.8828 (pp) REVERT: B 200 MET cc_start: 0.8932 (tpp) cc_final: 0.8729 (tpt) REVERT: B 494 LYS cc_start: 0.8201 (pttp) cc_final: 0.7814 (mtmt) REVERT: B 733 MET cc_start: 0.9074 (mtp) cc_final: 0.8736 (mtp) REVERT: E 121 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7366 (tpt) REVERT: F 84 GLU cc_start: 0.8066 (mp0) cc_final: 0.7636 (mp0) REVERT: H 55 LYS cc_start: 0.9197 (mttt) cc_final: 0.8844 (mttp) REVERT: I 33 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8281 (mmp-170) REVERT: I 67 GLN cc_start: 0.8972 (mp10) cc_final: 0.8485 (mp10) REVERT: I 82 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8119 (mm-30) REVERT: I 99 SER cc_start: 0.8921 (p) cc_final: 0.8680 (p) REVERT: I 122 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8715 (mtm-85) REVERT: K 24 ASP cc_start: 0.8584 (t0) cc_final: 0.8310 (t0) REVERT: L 31 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8401 (ptp90) REVERT: U 236 MET cc_start: 0.9121 (tpp) cc_final: 0.8857 (tpp) REVERT: U 261 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4808 (m-10) outliers start: 36 outliers final: 13 residues processed: 353 average time/residue: 1.5462 time to fit residues: 654.8455 Evaluate side-chains 314 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL 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 1282 ASP Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 261 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 178 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 149 optimal weight: 30.0000 chunk 374 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 369 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A1093 GLN ** A1251 ASN ** 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** ** 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 = 0.3581 r_free = 0.3581 target = 0.092636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056833 restraints weight = 78898.872| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.98 r_work: 0.2648 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 35005 Z= 0.237 Angle : 0.624 14.395 47643 Z= 0.323 Chirality : 0.046 0.238 5328 Planarity : 0.004 0.050 5878 Dihedral : 14.169 179.970 5394 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.51 % Allowed : 9.71 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4022 helix: 1.10 (0.14), residues: 1457 sheet: 0.07 (0.21), residues: 616 loop : -0.55 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS I 100 PHE 0.018 0.002 PHE C 63 TYR 0.016 0.001 TYR U 158 ARG 0.008 0.000 ARG F 100 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1469) hydrogen bonds : angle 4.75655 ( 4108) metal coordination : bond 0.00867 ( 19) metal coordination : angle 4.50550 ( 21) SS BOND : bond 0.00517 ( 8) SS BOND : angle 3.24989 ( 16) covalent geometry : bond 0.00550 (34978) covalent geometry : angle 0.61383 (47606) *********************** 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 371 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8342 (p-80) cc_final: 0.7883 (p-80) REVERT: A 334 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7075 (ppt-90) REVERT: A 1486 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.6391 (tt) REVERT: B 293 GLU cc_start: 0.8999 (mp0) cc_final: 0.8760 (mp0) REVERT: B 347 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8277 (tpt) REVERT: B 494 LYS cc_start: 0.8254 (pttp) cc_final: 0.7746 (mtmm) REVERT: B 733 MET cc_start: 0.9011 (mtp) cc_final: 0.8677 (mtp) REVERT: B 840 MET cc_start: 0.7292 (mmm) cc_final: 0.7008 (ttt) REVERT: E 70 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: F 82 GLU cc_start: 0.7865 (pp20) cc_final: 0.7546 (pp20) REVERT: F 83 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8978 (pp) REVERT: F 84 GLU cc_start: 0.8187 (mp0) cc_final: 0.7947 (mp0) REVERT: F 86 GLU cc_start: 0.7925 (mp0) cc_final: 0.7169 (mp0) REVERT: H 55 LYS cc_start: 0.9178 (mttt) cc_final: 0.8796 (mttm) REVERT: H 95 LYS cc_start: 0.9291 (ptmt) cc_final: 0.8942 (ptmm) REVERT: I 33 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8406 (mmp-170) REVERT: I 67 GLN cc_start: 0.8988 (mp10) cc_final: 0.8464 (mp10) REVERT: I 82 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7767 (mm-30) REVERT: K 24 ASP cc_start: 0.8551 (t0) cc_final: 0.8232 (t0) REVERT: K 97 GLU cc_start: 0.8187 (tt0) cc_final: 0.7887 (tt0) REVERT: L 31 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8483 (ptp90) REVERT: U 236 MET cc_start: 0.9138 (tpp) cc_final: 0.8855 (tpp) REVERT: U 250 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7802 (mmm) outliers start: 54 outliers final: 16 residues processed: 347 average time/residue: 1.5592 time to fit residues: 646.3577 Evaluate side-chains 315 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 865 ILE Chi-restraints excluded: chain A residue 1186 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 B residue 347 MET 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 E residue 96 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain H residue 47 ILE 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 U residue 161 ILE 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 255 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 331 optimal weight: 0.0070 chunk 56 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1251 ASN ** 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 C 108 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 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 = 0.3591 r_free = 0.3591 target = 0.093170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.057427 restraints weight = 77930.644| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.97 r_work: 0.2669 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35005 Z= 0.161 Angle : 0.571 9.857 47643 Z= 0.296 Chirality : 0.044 0.334 5328 Planarity : 0.004 0.043 5878 Dihedral : 14.133 178.472 5391 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.62 % Allowed : 11.06 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4022 helix: 1.33 (0.14), residues: 1449 sheet: 0.08 (0.21), residues: 623 loop : -0.47 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 27 HIS 0.005 0.001 HIS B 387 PHE 0.014 0.001 PHE C 21 TYR 0.018 0.001 TYR F 115 ARG 0.007 0.000 ARG U 246 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1469) hydrogen bonds : angle 4.55747 ( 4108) metal coordination : bond 0.00701 ( 19) metal coordination : angle 3.98494 ( 21) SS BOND : bond 0.00626 ( 8) SS BOND : angle 2.80162 ( 16) covalent geometry : bond 0.00369 (34978) covalent geometry : angle 0.56257 (47606) *********************** 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 371 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8328 (p-80) cc_final: 0.7864 (p-80) REVERT: A 334 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7179 (ppt-90) REVERT: A 769 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8578 (mtt) REVERT: A 1254 LYS cc_start: 0.7403 (tttt) cc_final: 0.7101 (OUTLIER) REVERT: A 1428 MET cc_start: 0.8878 (mtp) cc_final: 0.8580 (ttp) REVERT: A 1486 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6409 (tt) REVERT: B 293 GLU cc_start: 0.8966 (mp0) cc_final: 0.8760 (mp0) REVERT: B 347 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8264 (tpt) REVERT: B 733 MET cc_start: 0.8867 (mtp) cc_final: 0.8629 (mtp) REVERT: B 840 MET cc_start: 0.7266 (mmm) cc_final: 0.6979 (ttt) REVERT: C 5 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7938 (OUTLIER) REVERT: E 70 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: F 82 GLU cc_start: 0.7900 (pp20) cc_final: 0.7524 (pp20) REVERT: F 84 GLU cc_start: 0.8261 (mp0) cc_final: 0.7942 (mp0) REVERT: H 55 LYS cc_start: 0.9209 (mttt) cc_final: 0.8843 (mttm) REVERT: H 95 LYS cc_start: 0.9307 (ptmt) cc_final: 0.8966 (ptmm) REVERT: I 33 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8422 (mmp-170) REVERT: I 67 GLN cc_start: 0.8957 (mp10) cc_final: 0.8463 (mp10) REVERT: J 36 ASP cc_start: 0.8994 (m-30) cc_final: 0.8789 (m-30) REVERT: K 24 ASP cc_start: 0.8533 (t0) cc_final: 0.8239 (t0) REVERT: K 97 GLU cc_start: 0.8148 (tt0) cc_final: 0.7815 (tt0) REVERT: L 31 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8514 (ptp90) REVERT: L 50 LYS cc_start: 0.9362 (mptp) cc_final: 0.9145 (mmmt) REVERT: L 58 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8127 (mtt-85) REVERT: U 189 ASN cc_start: 0.9213 (p0) cc_final: 0.8973 (p0) REVERT: U 236 MET cc_start: 0.9118 (tpp) cc_final: 0.8835 (tpp) outliers start: 58 outliers final: 18 residues processed: 347 average time/residue: 1.7905 time to fit residues: 748.3411 Evaluate side-chains 314 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 7.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 MET 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 347 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 919 CYS 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 E residue 185 ILE 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 U residue 161 ILE 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 191 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 350 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 chunk 355 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1251 ASN ** 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 ** 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 = 0.3611 r_free = 0.3611 target = 0.094290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058702 restraints weight = 78087.739| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.99 r_work: 0.2703 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35005 Z= 0.116 Angle : 0.558 10.431 47643 Z= 0.287 Chirality : 0.043 0.290 5328 Planarity : 0.003 0.041 5878 Dihedral : 14.069 177.023 5391 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.37 % Allowed : 11.89 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4022 helix: 1.51 (0.14), residues: 1441 sheet: 0.15 (0.21), residues: 615 loop : -0.40 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.004 0.000 HIS A 84 PHE 0.028 0.001 PHE A 458 TYR 0.018 0.001 TYR F 115 ARG 0.010 0.000 ARG I 122 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1469) hydrogen bonds : angle 4.39482 ( 4108) metal coordination : bond 0.00557 ( 19) metal coordination : angle 3.74126 ( 21) SS BOND : bond 0.00498 ( 8) SS BOND : angle 3.46918 ( 16) covalent geometry : bond 0.00257 (34978) covalent geometry : angle 0.54884 (47606) *********************** 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: 49 poor density : 317 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8306 (p-80) cc_final: 0.7847 (p-80) REVERT: A 334 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7101 (ppt-90) REVERT: A 769 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8495 (mtt) REVERT: A 1254 LYS cc_start: 0.7371 (tttt) cc_final: 0.7087 (mmmt) REVERT: A 1351 ASP cc_start: 0.7656 (t70) cc_final: 0.7326 (t0) REVERT: A 1428 MET cc_start: 0.8825 (mtp) cc_final: 0.8543 (ttp) REVERT: A 1486 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6361 (tt) REVERT: B 293 GLU cc_start: 0.8947 (mp0) cc_final: 0.8732 (mp0) REVERT: B 733 MET cc_start: 0.8750 (mtp) cc_final: 0.8494 (mtp) REVERT: B 1132 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9054 (m) REVERT: E 70 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: F 82 GLU cc_start: 0.7955 (pp20) cc_final: 0.7654 (pp20) REVERT: F 83 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (pp) REVERT: F 84 GLU cc_start: 0.8381 (mp0) cc_final: 0.7983 (mp0) REVERT: H 28 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8850 (pp) REVERT: I 33 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8364 (mmp-170) REVERT: I 67 GLN cc_start: 0.8945 (mp10) cc_final: 0.8478 (mp10) REVERT: K 24 ASP cc_start: 0.8524 (t0) cc_final: 0.8230 (t0) REVERT: K 97 GLU cc_start: 0.8152 (tt0) cc_final: 0.7833 (tt0) REVERT: L 31 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8554 (ptp90) REVERT: L 50 LYS cc_start: 0.9364 (mptp) cc_final: 0.9135 (mmmt) REVERT: L 56 ASP cc_start: 0.8035 (t0) cc_final: 0.7721 (t0) REVERT: L 58 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8128 (mtt-85) REVERT: U 158 TYR cc_start: 0.7494 (p90) cc_final: 0.7287 (p90) REVERT: U 189 ASN cc_start: 0.9171 (p0) cc_final: 0.8920 (p0) REVERT: U 223 MET cc_start: 0.8830 (mmm) cc_final: 0.8319 (mpp) REVERT: U 236 MET cc_start: 0.9123 (tpp) cc_final: 0.8783 (tpp) REVERT: U 250 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7868 (mmm) outliers start: 49 outliers final: 12 residues processed: 345 average time/residue: 1.5714 time to fit residues: 651.4321 Evaluate side-chains 317 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU 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 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1486 ILE 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 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 K residue 20 THR Chi-restraints excluded: chain L residue 31 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 343 optimal weight: 6.9990 chunk 369 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 153 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN A1194 ASN A1251 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B1021 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN G 53 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.056403 restraints weight = 77978.123| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.98 r_work: 0.2641 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35005 Z= 0.228 Angle : 0.615 10.321 47643 Z= 0.316 Chirality : 0.045 0.366 5328 Planarity : 0.004 0.042 5878 Dihedral : 14.100 178.575 5391 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.60 % Allowed : 12.57 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4022 helix: 1.44 (0.14), residues: 1454 sheet: 0.10 (0.21), residues: 609 loop : -0.42 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 27 HIS 0.005 0.001 HIS A 84 PHE 0.018 0.001 PHE G 44 TYR 0.018 0.001 TYR F 115 ARG 0.016 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1469) hydrogen bonds : angle 4.52144 ( 4108) metal coordination : bond 0.00783 ( 19) metal coordination : angle 4.21822 ( 21) SS BOND : bond 0.00768 ( 8) SS BOND : angle 3.03577 ( 16) covalent geometry : bond 0.00535 (34978) covalent geometry : angle 0.60667 (47606) *********************** 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 355 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8346 (p-80) cc_final: 0.7883 (p-80) REVERT: A 334 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7568 (tmm160) REVERT: A 769 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8718 (mtt) REVERT: A 1254 LYS cc_start: 0.7577 (tttt) cc_final: 0.7293 (mmmt) REVERT: A 1428 MET cc_start: 0.8901 (mtp) cc_final: 0.8581 (ttp) REVERT: A 1486 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6353 (tt) REVERT: B 347 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8290 (tpt) REVERT: B 733 MET cc_start: 0.8942 (mtp) cc_final: 0.8701 (mtp) REVERT: C 5 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (p0) REVERT: D 62 MET cc_start: 0.7440 (mmt) cc_final: 0.7151 (mpp) REVERT: E 70 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: F 82 GLU cc_start: 0.8024 (pp20) cc_final: 0.7640 (pp20) REVERT: F 83 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8990 (pp) REVERT: F 84 GLU cc_start: 0.8429 (mp0) cc_final: 0.8076 (mp0) REVERT: F 86 GLU cc_start: 0.7994 (mp0) cc_final: 0.7301 (mp0) REVERT: H 28 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8903 (pp) REVERT: I 28 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7592 (tp30) REVERT: I 33 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8475 (mmp-170) REVERT: I 67 GLN cc_start: 0.8963 (mp10) cc_final: 0.8488 (mp10) REVERT: K 24 ASP cc_start: 0.8516 (t0) cc_final: 0.8198 (t0) REVERT: K 97 GLU cc_start: 0.8233 (tt0) cc_final: 0.7862 (tt0) REVERT: L 31 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8607 (ptp90) REVERT: U 236 MET cc_start: 0.9127 (tpp) cc_final: 0.8786 (tpp) REVERT: U 239 ASN cc_start: 0.9380 (t0) cc_final: 0.8951 (t0) REVERT: U 250 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7879 (mmm) outliers start: 57 outliers final: 22 residues processed: 334 average time/residue: 2.2257 time to fit residues: 909.5361 Evaluate side-chains 313 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU 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 787 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1374 VAL 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 860 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 F residue 83 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 72 TYR 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 K residue 25 THR Chi-restraints excluded: chain L residue 31 ARG 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 211 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** 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 ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN K 55 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 = 0.3602 r_free = 0.3602 target = 0.093833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058290 restraints weight = 78203.809| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.98 r_work: 0.2690 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35005 Z= 0.118 Angle : 0.574 11.099 47643 Z= 0.294 Chirality : 0.043 0.360 5328 Planarity : 0.004 0.044 5878 Dihedral : 14.069 176.951 5391 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 1.34 % Allowed : 13.46 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 4022 helix: 1.59 (0.14), residues: 1444 sheet: 0.19 (0.21), residues: 610 loop : -0.35 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.004 0.000 HIS A 84 PHE 0.020 0.001 PHE G 44 TYR 0.017 0.001 TYR F 115 ARG 0.013 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 1469) hydrogen bonds : angle 4.38016 ( 4108) metal coordination : bond 0.00566 ( 19) metal coordination : angle 4.10598 ( 21) SS BOND : bond 0.00681 ( 8) SS BOND : angle 2.72168 ( 16) covalent geometry : bond 0.00259 (34978) covalent geometry : angle 0.56510 (47606) *********************** 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 353 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 3.612 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: 0.5491 (mmt) cc_final: 0.5076 (mmp) REVERT: A 301 HIS cc_start: 0.8309 (p-80) cc_final: 0.7839 (p-80) REVERT: A 334 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7075 (ppt-90) REVERT: A 769 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8520 (mtt) REVERT: A 1254 LYS cc_start: 0.7554 (tttt) cc_final: 0.7297 (mmmt) REVERT: A 1428 MET cc_start: 0.8856 (mtp) cc_final: 0.8602 (ttp) REVERT: A 1486 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6349 (tt) REVERT: B 494 LYS cc_start: 0.8415 (pttm) cc_final: 0.8108 (mtmm) REVERT: B 733 MET cc_start: 0.8743 (mtp) cc_final: 0.8472 (mtp) REVERT: E 70 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: E 72 MET cc_start: 0.8691 (ttt) cc_final: 0.8440 (ttm) REVERT: F 82 GLU cc_start: 0.8086 (pp20) cc_final: 0.7670 (pp20) REVERT: F 83 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8914 (pp) REVERT: F 84 GLU cc_start: 0.8510 (mp0) cc_final: 0.8091 (mp0) REVERT: F 86 GLU cc_start: 0.7913 (mp0) cc_final: 0.7697 (mp0) REVERT: H 28 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8823 (pp) REVERT: I 33 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8505 (mtp180) REVERT: I 63 ASP cc_start: 0.8883 (m-30) cc_final: 0.8657 (t0) REVERT: I 67 GLN cc_start: 0.8929 (mp10) cc_final: 0.8222 (mp10) REVERT: K 24 ASP cc_start: 0.8494 (t0) cc_final: 0.8176 (t0) REVERT: K 97 GLU cc_start: 0.8231 (tt0) cc_final: 0.7906 (tt0) REVERT: L 58 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8268 (mtt-85) REVERT: U 189 ASN cc_start: 0.9145 (p0) cc_final: 0.8893 (p0) REVERT: U 223 MET cc_start: 0.8863 (mmm) cc_final: 0.8374 (mpp) REVERT: U 236 MET cc_start: 0.9133 (tpp) cc_final: 0.8733 (tpp) REVERT: U 239 ASN cc_start: 0.9371 (t0) cc_final: 0.8880 (t0) outliers start: 48 outliers final: 21 residues processed: 337 average time/residue: 1.5976 time to fit residues: 645.6080 Evaluate side-chains 317 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU 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 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 MET 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 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 C residue 109 GLU 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 H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain U residue 187 TYR 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 211 optimal weight: 0.0770 chunk 268 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 345 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 264 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 212 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN K 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059760 restraints weight = 77824.682| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.99 r_work: 0.2726 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35005 Z= 0.105 Angle : 0.566 11.461 47643 Z= 0.288 Chirality : 0.043 0.369 5328 Planarity : 0.003 0.042 5878 Dihedral : 14.006 175.374 5391 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 0.90 % Allowed : 14.27 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 4022 helix: 1.72 (0.14), residues: 1433 sheet: 0.14 (0.21), residues: 622 loop : -0.29 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 22 HIS 0.008 0.001 HIS C 265 PHE 0.022 0.001 PHE G 44 TYR 0.015 0.001 TYR U 158 ARG 0.010 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 1469) hydrogen bonds : angle 4.23110 ( 4108) metal coordination : bond 0.00467 ( 19) metal coordination : angle 3.69017 ( 21) SS BOND : bond 0.00607 ( 8) SS BOND : angle 2.44899 ( 16) covalent geometry : bond 0.00230 (34978) covalent geometry : angle 0.55879 (47606) *********************** 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 351 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 319 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5523 (mmt) cc_final: 0.5177 (mmp) REVERT: A 301 HIS cc_start: 0.8305 (p-80) cc_final: 0.7835 (p-80) REVERT: A 334 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7233 (ppt-90) REVERT: A 769 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: A 1292 MET cc_start: 0.8073 (mmp) cc_final: 0.7849 (mtm) REVERT: A 1451 MET cc_start: 0.9108 (mmm) cc_final: 0.8822 (mmm) REVERT: A 1486 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6310 (tt) REVERT: B 108 MET cc_start: 0.8987 (ttp) cc_final: 0.8602 (ptm) REVERT: B 1132 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9029 (m) REVERT: C 164 TYR cc_start: 0.8997 (m-80) cc_final: 0.8768 (m-80) REVERT: E 70 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: F 82 GLU cc_start: 0.8089 (pp20) cc_final: 0.7685 (pp20) REVERT: F 83 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8903 (pp) REVERT: F 84 GLU cc_start: 0.8523 (mp0) cc_final: 0.8088 (mp0) REVERT: F 86 GLU cc_start: 0.7908 (mp0) cc_final: 0.7683 (mp0) REVERT: H 28 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8827 (pp) REVERT: I 63 ASP cc_start: 0.8931 (m-30) cc_final: 0.8667 (t0) REVERT: I 67 GLN cc_start: 0.8870 (mp10) cc_final: 0.8179 (mp10) REVERT: K 24 ASP cc_start: 0.8458 (t0) cc_final: 0.8161 (t0) REVERT: K 97 GLU cc_start: 0.8280 (tt0) cc_final: 0.7986 (tt0) REVERT: U 189 ASN cc_start: 0.9147 (p0) cc_final: 0.8902 (p0) REVERT: U 236 MET cc_start: 0.9138 (tpp) cc_final: 0.8811 (tpp) outliers start: 32 outliers final: 16 residues processed: 337 average time/residue: 1.6044 time to fit residues: 653.5385 Evaluate side-chains 322 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 872 MET 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 908 MET 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 E residue 168 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 117 MET 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 K residue 20 THR Chi-restraints excluded: chain U residue 250 MET Chi-restraints excluded: chain U residue 261 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 321 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 374 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 189 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.094169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058703 restraints weight = 78584.497| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.99 r_work: 0.2703 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35005 Z= 0.136 Angle : 0.581 11.753 47643 Z= 0.297 Chirality : 0.043 0.375 5328 Planarity : 0.003 0.044 5878 Dihedral : 13.992 176.160 5391 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 0.98 % Allowed : 14.81 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 4022 helix: 1.70 (0.14), residues: 1446 sheet: 0.15 (0.21), residues: 622 loop : -0.28 (0.15), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 27 HIS 0.003 0.001 HIS A 84 PHE 0.023 0.001 PHE G 44 TYR 0.024 0.001 TYR U 158 ARG 0.011 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1469) hydrogen bonds : angle 4.26746 ( 4108) metal coordination : bond 0.00461 ( 19) metal coordination : angle 3.63111 ( 21) SS BOND : bond 0.00638 ( 8) SS BOND : angle 2.51699 ( 16) covalent geometry : bond 0.00313 (34978) covalent geometry : angle 0.57478 (47606) *********************** 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 332 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5581 (mmt) cc_final: 0.5280 (mmp) REVERT: A 334 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7127 (ppt-90) REVERT: A 769 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8602 (mtt) REVERT: A 1451 MET cc_start: 0.9140 (mmm) cc_final: 0.8859 (mmm) REVERT: A 1486 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6369 (tt) REVERT: B 108 MET cc_start: 0.8993 (ttp) cc_final: 0.8606 (ptm) REVERT: B 494 LYS cc_start: 0.8386 (pttm) cc_final: 0.8111 (mtmm) REVERT: C 164 TYR cc_start: 0.9045 (m-80) cc_final: 0.8796 (m-80) REVERT: E 70 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: F 82 GLU cc_start: 0.8123 (pp20) cc_final: 0.7759 (pp20) REVERT: F 83 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8943 (pp) REVERT: F 84 GLU cc_start: 0.8539 (mp0) cc_final: 0.8110 (mp0) REVERT: F 86 GLU cc_start: 0.7897 (mp0) cc_final: 0.7673 (mp0) REVERT: H 28 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8830 (pp) REVERT: I 63 ASP cc_start: 0.8947 (m-30) cc_final: 0.8674 (t0) REVERT: I 67 GLN cc_start: 0.8868 (mp10) cc_final: 0.8155 (mp10) REVERT: K 24 ASP cc_start: 0.8538 (t0) cc_final: 0.8270 (t0) REVERT: K 97 GLU cc_start: 0.8248 (tt0) cc_final: 0.7943 (tt0) REVERT: U 189 ASN cc_start: 0.9165 (p0) cc_final: 0.8921 (p0) REVERT: U 236 MET cc_start: 0.9136 (tpp) cc_final: 0.8810 (tpp) outliers start: 35 outliers final: 20 residues processed: 322 average time/residue: 1.5516 time to fit residues: 598.2398 Evaluate side-chains 316 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1231 ILE 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 C residue 5 ASN Chi-restraints excluded: chain C residue 90 CYS 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 H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain U residue 187 TYR Chi-restraints excluded: chain U residue 250 MET Chi-restraints excluded: chain U residue 261 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 286 optimal weight: 30.0000 chunk 179 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 400 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS K 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058198 restraints weight = 77956.881| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.96 r_work: 0.2691 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35005 Z= 0.154 Angle : 0.608 16.454 47643 Z= 0.309 Chirality : 0.044 0.383 5328 Planarity : 0.004 0.045 5878 Dihedral : 14.012 176.759 5391 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 0.87 % Allowed : 15.09 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 4022 helix: 1.69 (0.14), residues: 1436 sheet: 0.15 (0.21), residues: 611 loop : -0.27 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.005 0.001 HIS I 100 PHE 0.025 0.001 PHE G 44 TYR 0.021 0.001 TYR U 158 ARG 0.011 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1469) hydrogen bonds : angle 4.32897 ( 4108) metal coordination : bond 0.00510 ( 19) metal coordination : angle 3.74372 ( 21) SS BOND : bond 0.00646 ( 8) SS BOND : angle 2.58244 ( 16) covalent geometry : bond 0.00357 (34978) covalent geometry : angle 0.60088 (47606) ********************** 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 327 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 3.624 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: 0.5549 (mmt) cc_final: 0.5255 (mmp) REVERT: A 334 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7558 (tmm160) REVERT: A 769 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: A 1451 MET cc_start: 0.9135 (mmm) cc_final: 0.8879 (mmm) REVERT: A 1486 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6394 (tt) REVERT: B 108 MET cc_start: 0.8971 (ttp) cc_final: 0.8594 (ptm) REVERT: B 494 LYS cc_start: 0.8373 (pttm) cc_final: 0.8095 (mtmm) REVERT: C 164 TYR cc_start: 0.9084 (m-80) cc_final: 0.8818 (m-80) REVERT: E 70 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: F 82 GLU cc_start: 0.8164 (pp20) cc_final: 0.7804 (pp20) REVERT: F 83 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8949 (pp) REVERT: F 84 GLU cc_start: 0.8551 (mp0) cc_final: 0.8118 (mp0) REVERT: F 86 GLU cc_start: 0.7895 (mp0) cc_final: 0.7670 (mp0) REVERT: H 28 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (pp) REVERT: I 63 ASP cc_start: 0.8936 (m-30) cc_final: 0.8653 (t0) REVERT: I 67 GLN cc_start: 0.8849 (mp10) cc_final: 0.8447 (mp10) REVERT: J 28 GLU cc_start: 0.8382 (pp20) cc_final: 0.8182 (pp20) REVERT: K 24 ASP cc_start: 0.8523 (t0) cc_final: 0.8219 (t0) REVERT: K 97 GLU cc_start: 0.8250 (tt0) cc_final: 0.7945 (tt0) REVERT: U 189 ASN cc_start: 0.9108 (p0) cc_final: 0.8867 (p0) REVERT: U 236 MET cc_start: 0.9131 (tpp) cc_final: 0.8794 (tpp) outliers start: 31 outliers final: 20 residues processed: 318 average time/residue: 1.7918 time to fit residues: 689.5405 Evaluate side-chains 311 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1186 VAL 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 C residue 5 ASN Chi-restraints excluded: chain C residue 90 CYS 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 H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 41 TYR 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 191 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 406 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 237 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 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 = 0.3585 r_free = 0.3585 target = 0.092830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.057349 restraints weight = 78447.575| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.98 r_work: 0.2666 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 35005 Z= 0.192 Angle : 0.633 15.299 47643 Z= 0.322 Chirality : 0.045 0.379 5328 Planarity : 0.004 0.060 5878 Dihedral : 14.044 177.375 5391 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 0.92 % Allowed : 15.14 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 4022 helix: 1.60 (0.14), residues: 1449 sheet: 0.21 (0.21), residues: 600 loop : -0.31 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.027 0.001 HIS I 100 PHE 0.025 0.001 PHE G 44 TYR 0.017 0.001 TYR F 115 ARG 0.014 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 1469) hydrogen bonds : angle 4.39232 ( 4108) metal coordination : bond 0.00610 ( 19) metal coordination : angle 3.93313 ( 21) SS BOND : bond 0.00672 ( 8) SS BOND : angle 2.68066 ( 16) covalent geometry : bond 0.00448 (34978) covalent geometry : angle 0.62560 (47606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26105.30 seconds wall clock time: 459 minutes 24.05 seconds (27564.05 seconds total)