Starting phenix.real_space_refine on Tue Aug 26 10:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei4_48076/08_2025/9ei4_48076.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 222 5.16 5 C 22473 2.51 5 N 6310 2.21 5 O 6788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35854 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11317 Classifications: {'peptide': 1428} Link IDs: {'PTRANS': 70, 'TRANS': 1357} Chain breaks: 4 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: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "U" Number of atoms: 3692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 472, 3686 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 453} Chain breaks: 9 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 472, 3686 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 453} Chain breaks: 9 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3743 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 61.717 71.558 77.551 1.00 45.21 S ATOM 486 SG CYS A 74 62.077 75.217 76.978 1.00 44.36 S ATOM 533 SG CYS A 81 65.183 73.061 77.846 1.00 44.06 S ATOM 768 SG CYS A 111 75.975 86.557 121.242 1.00 62.88 S ATOM 796 SG CYS A 114 73.154 89.089 121.354 1.00 66.01 S ATOM 1109 SG CYS A 154 76.592 89.600 123.141 1.00 73.52 S ATOM 1142 SG CYS A 184 73.884 86.963 124.313 1.00 76.31 S ATOM 19949 SG CYS B1119 63.722 88.813 85.330 1.00 44.02 S ATOM 19971 SG CYS B1122 65.513 86.854 88.047 1.00 43.65 S ATOM 20086 SG CYS B1137 62.814 85.202 85.994 1.00 48.53 S ATOM 20107 SG CYS B1140 61.990 87.601 88.708 1.00 53.95 S ATOM 21074 SG CYS C 88 92.678 52.924 20.457 1.00 52.78 S ATOM 21087 SG CYS C 90 90.337 50.564 22.165 1.00 57.39 S ATOM 21122 SG CYS C 94 93.009 49.267 19.754 1.00 48.10 S ATOM 21144 SG CYS C 97 94.102 50.616 23.118 1.00 46.32 S ATOM 28380 SG CYS I 17 130.426 53.001 137.912 1.00 87.54 S ATOM 28404 SG CYS I 20 126.748 52.464 137.020 1.00 84.47 S ATOM 28565 SG CYS I 39 127.972 55.876 137.324 1.00 84.94 S ATOM 28590 SG CYS I 42 127.652 53.663 140.467 1.00 81.99 S ATOM 28942 SG CYS I 86 158.266 52.859 104.479 1.00 57.21 S ATOM 28966 SG CYS I 89 159.486 49.302 103.806 1.00 59.16 S ATOM 29170 SG CYS I 114 156.651 50.633 101.781 1.00 54.71 S ATOM 29205 SG CYS I 119 156.288 49.643 105.422 1.00 58.36 S ATOM 29315 SG CYS J 7 120.334 51.346 40.404 1.00 21.15 S ATOM 29339 SG CYS J 10 121.227 52.732 37.010 1.00 21.60 S ATOM 29603 SG CYS J 44 123.402 53.440 40.183 1.00 22.57 S ATOM 29609 SG CYS J 45 123.440 50.222 38.233 1.00 21.63 S ATOM 30755 SG CYS L 19 91.839 24.797 59.213 1.00 45.34 S ATOM 30774 SG CYS L 22 91.763 21.649 56.985 1.00 46.13 S ATOM 30891 SG CYS L 36 89.170 22.410 59.332 1.00 49.92 S ATOM 30917 SG CYS L 39 92.773 21.619 60.807 1.00 52.41 S Time building chain proxies: 7.33, per 1000 atoms: 0.20 Number of scatterers: 35854 At special positions: 0 Unit cell: (180.256, 148.816, 191.784, 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 8 29.99 S 222 16.00 P 52 15.00 Mg 1 11.99 O 6788 8.00 N 6310 7.00 C 22473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 431 " - pdb=" SG CYS U 434 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8238 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 50 sheets defined 40.0% alpha, 15.9% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.845A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.667A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.503A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 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 488 through 493 removed outlier: 3.616A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.928A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.853A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.075A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 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 816 through 821 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.886A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.535A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.511A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 3.896A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1186 through 1189 Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1201 through 1205 removed outlier: 4.285A pdb=" N VAL A1204 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.556A 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 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.747A 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 1430 Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.531A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1476 through 1482' Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.530A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 removed outlier: 3.504A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.769A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.612A 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 455 through 459 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.558A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.530A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 4.111A 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 removed outlier: 3.801A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.681A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.092A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.732A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 994 Processing helix chain 'B' and resid 1007 through 1017 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 40 Processing helix chain 'C' and resid 60 through 70 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: 3.566A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.560A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 4.055A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.867A 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 137 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: 3.550A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.518A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) 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 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.035A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.939A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.630A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 61 removed outlier: 4.270A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.217A 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 19 through 24 removed outlier: 3.679A pdb=" N VAL U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 19 through 24' Processing helix chain 'U' and resid 32 through 43 removed outlier: 3.699A pdb=" N SER U 36 " --> pdb=" O PRO U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 removed outlier: 3.584A pdb=" N CYS U 61 " --> pdb=" O GLY U 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) Proline residue: U 65 - end of helix Processing helix chain 'U' and resid 79 through 92 Processing helix chain 'U' and resid 175 through 183 Processing helix chain 'U' and resid 196 through 206 Processing helix chain 'U' and resid 237 through 248 Processing helix chain 'U' and resid 270 through 282 removed outlier: 3.946A pdb=" N GLN U 274 " --> pdb=" O GLU U 270 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU U 275 " --> pdb=" O ALA U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 294 through 307 Processing helix chain 'U' and resid 339 through 348 Processing helix chain 'U' and resid 364 through 381 Processing helix chain 'U' and resid 393 through 407 Processing helix chain 'U' and resid 411 through 421 Processing helix chain 'U' and resid 431 through 436 Processing helix chain 'U' and resid 436 through 451 Processing helix chain 'U' and resid 499 through 514 removed outlier: 4.152A pdb=" N LEU U 514 " --> pdb=" O LYS U 510 " (cutoff:3.500A) Processing helix chain 'U' and resid 546 through 569 Processing helix chain 'U' and resid 572 through 590 removed outlier: 4.126A pdb=" N ALA U 578 " --> pdb=" O ALA U 574 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 3.501A pdb=" N LEU A 90 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.698A pdb=" N ARG A 190 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 266 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.699A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.089A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.861A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.596A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.748A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1335 through 1339 Processing sheet with id=AB7, first strand: chain 'A' and resid 1246 through 1247 removed outlier: 4.421A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 8.482A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.445A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.445A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.615A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.605A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC9, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.487A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.633A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.078A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 828 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.658A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1129 removed outlier: 3.666A pdb=" N ASN B1129 " --> pdb=" O THR B1134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.537A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.537A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.683A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.526A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.679A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.752A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 12 removed outlier: 5.318A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.525A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'L' and resid 16 through 17 Processing sheet with id=AF3, first strand: chain 'U' and resid 97 through 98 Processing sheet with id=AF4, first strand: chain 'U' and resid 228 through 231 removed outlier: 3.590A pdb=" N TYR U 363 " --> pdb=" O GLN U 230 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 262 through 264 removed outlier: 6.627A pdb=" N GLY U 262 " --> pdb=" O ILE U 313 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA U 315 " --> pdb=" O GLY U 262 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL U 264 " --> pdb=" O ALA U 315 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS U 287 " --> pdb=" O VAL U 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1478 hydrogen bonds defined for protein. 4143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10746 1.33 - 1.45: 5902 1.45 - 1.57: 19537 1.57 - 1.69: 100 1.69 - 1.81: 344 Bond restraints: 36629 Sorted by residual: bond pdb=" C3' ADP U1000 " pdb=" C4' ADP U1000 " ideal model delta sigma weight residual 1.524 1.306 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C4' ADP U1000 " pdb=" O4' ADP U1000 " ideal model delta sigma weight residual 1.426 1.615 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C4 ADP U1000 " pdb=" C5 ADP U1000 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C1' ADP U1000 " pdb=" O4' ADP U1000 " ideal model delta sigma weight residual 1.426 1.306 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C5 ADP U1000 " pdb=" C6 ADP U1000 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 36624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 49575 4.07 - 8.13: 114 8.13 - 12.20: 4 12.20 - 16.27: 1 16.27 - 20.33: 1 Bond angle restraints: 49695 Sorted by residual: angle pdb=" C1' ADP U1000 " pdb=" N9 ADP U1000 " pdb=" C8 ADP U1000 " ideal model delta sigma weight residual 126.00 105.67 20.33 3.00e+00 1.11e-01 4.59e+01 angle pdb=" C ALA B 241 " pdb=" CA ALA B 241 " pdb=" CB ALA B 241 " ideal model delta sigma weight residual 115.79 109.29 6.50 1.19e+00 7.06e-01 2.98e+01 angle pdb=" C1' ADP U1000 " pdb=" N9 ADP U1000 " pdb=" C4 ADP U1000 " ideal model delta sigma weight residual 126.00 141.43 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N PRO A 582 " pdb=" CA PRO A 582 " pdb=" C PRO A 582 " ideal model delta sigma weight residual 113.75 106.74 7.01 1.49e+00 4.50e-01 2.21e+01 angle pdb=" C ASP A1250 " pdb=" CA ASP A1250 " pdb=" CB ASP A1250 " ideal model delta sigma weight residual 115.79 110.47 5.32 1.19e+00 7.06e-01 2.00e+01 ... (remaining 49690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 21777 33.89 - 67.79: 537 67.79 - 101.68: 22 101.68 - 135.57: 1 135.57 - 169.47: 4 Dihedral angle restraints: 22341 sinusoidal: 9619 harmonic: 12722 Sorted by residual: dihedral pdb=" C5' ADP U1000 " pdb=" O5' ADP U1000 " pdb=" PA ADP U1000 " pdb=" O2A ADP U1000 " ideal model delta sinusoidal sigma weight residual -60.00 109.47 -169.47 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA GLY U 25 " pdb=" C GLY U 25 " pdb=" N PHE U 26 " pdb=" CA PHE U 26 " ideal model delta harmonic sigma weight residual 180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLU J 28 " pdb=" C GLU J 28 " pdb=" N TYR J 29 " pdb=" CA TYR J 29 " ideal model delta harmonic sigma weight residual -180.00 -147.62 -32.38 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 22338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 5292 0.101 - 0.202: 268 0.202 - 0.303: 2 0.303 - 0.403: 1 0.403 - 0.504: 2 Chirality restraints: 5565 Sorted by residual: chirality pdb=" P DC T 13 " pdb=" OP1 DC T 13 " pdb=" OP2 DC T 13 " pdb=" O5' DC T 13 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" P DG T 14 " pdb=" OP1 DG T 14 " pdb=" OP2 DG T 14 " pdb=" O5' DG T 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA VAL U 76 " pdb=" N VAL U 76 " pdb=" C VAL U 76 " pdb=" CB VAL U 76 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 5562 not shown) Planarity restraints: 6258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BSER U 77 " -0.035 2.00e-02 2.50e+03 7.02e-02 4.93e+01 pdb=" C BSER U 77 " 0.121 2.00e-02 2.50e+03 pdb=" O BSER U 77 " -0.045 2.00e-02 2.50e+03 pdb=" N PRO U 78 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.613 9.50e-02 1.11e+02 2.75e-01 4.61e+01 pdb=" NE ARG A 583 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL U 76 " 0.029 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C VAL U 76 " -0.105 2.00e-02 2.50e+03 pdb=" O VAL U 76 " 0.039 2.00e-02 2.50e+03 pdb=" N BSER U 77 " 0.036 2.00e-02 2.50e+03 ... (remaining 6255 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 280 2.49 - 3.09: 26320 3.09 - 3.69: 57737 3.69 - 4.30: 83400 4.30 - 4.90: 137953 Nonbonded interactions: 305690 Sorted by model distance: nonbonded pdb=" O3' C P 20 " pdb="MG MG A2003 " model vdw 1.882 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.971 2.170 nonbonded pdb=" OD2 ASP A 495 " pdb="MG MG A2003 " model vdw 2.034 2.170 nonbonded pdb=" O THR U 31 " pdb=" N GLN U 34 " model vdw 2.073 3.120 nonbonded pdb=" O PRO A 971 " pdb=" OG1 THR A 972 " model vdw 2.150 3.040 ... (remaining 305685 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 37.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.218 36662 Z= 0.343 Angle : 0.686 20.333 49742 Z= 0.360 Chirality : 0.049 0.504 5565 Planarity : 0.007 0.275 6258 Dihedral : 13.958 169.466 14100 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.87 % Favored : 92.83 % Rotamer: Outliers : 5.13 % Allowed : 8.58 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 4314 helix: 0.75 (0.13), residues: 1536 sheet: -0.67 (0.21), residues: 601 loop : -1.08 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 352 TYR 0.019 0.002 TYR J 43 PHE 0.021 0.002 PHE B 568 TRP 0.024 0.002 TRP B 27 HIS 0.006 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00754 (36629) covalent geometry : angle 0.67299 (49695) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.63935 ( 2) hydrogen bonds : bond 0.14565 ( 1505) hydrogen bonds : angle 6.27995 ( 4231) metal coordination : bond 0.01532 ( 32) metal coordination : angle 4.41345 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1009 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8155 (tp40) cc_final: 0.7945 (tp40) REVERT: A 27 SER cc_start: 0.8079 (t) cc_final: 0.7689 (p) REVERT: A 51 ARG cc_start: 0.6645 (ptp90) cc_final: 0.6314 (ptp90) REVERT: A 66 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: A 70 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7120 (mtp85) REVERT: A 89 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6488 (mm-30) REVERT: A 105 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7620 (mtmt) REVERT: A 110 VAL cc_start: 0.7066 (t) cc_final: 0.6649 (m) REVERT: A 133 SER cc_start: 0.7888 (m) cc_final: 0.7614 (p) REVERT: A 152 ASN cc_start: 0.7129 (t0) cc_final: 0.6702 (t0) REVERT: A 188 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7365 (mm-40) REVERT: A 238 MET cc_start: 0.8060 (mtp) cc_final: 0.7714 (mtt) REVERT: A 308 LYS cc_start: 0.7384 (tttm) cc_final: 0.7153 (tttm) REVERT: A 319 ASP cc_start: 0.7658 (t0) cc_final: 0.7323 (t0) REVERT: A 340 LYS cc_start: 0.8076 (tttt) cc_final: 0.7734 (ttmt) REVERT: A 347 GLU cc_start: 0.6760 (mp0) cc_final: 0.6414 (mp0) REVERT: A 417 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7925 (mtpt) REVERT: A 421 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7375 (mtt-85) REVERT: A 430 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7289 (mtm180) REVERT: A 499 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7691 (t0) REVERT: A 540 ASP cc_start: 0.7438 (m-30) cc_final: 0.7167 (m-30) REVERT: A 608 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7731 (t) REVERT: A 619 LYS cc_start: 0.8118 (ptmt) cc_final: 0.7898 (ptpt) REVERT: A 639 ILE cc_start: 0.8464 (mm) cc_final: 0.8250 (mm) REVERT: A 692 SER cc_start: 0.8360 (p) cc_final: 0.8048 (p) REVERT: A 697 LYS cc_start: 0.8077 (tptt) cc_final: 0.7842 (tptt) REVERT: A 715 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 759 SER cc_start: 0.7490 (p) cc_final: 0.7150 (t) REVERT: A 803 LYS cc_start: 0.8181 (tptt) cc_final: 0.7871 (tptm) REVERT: A 818 GLU cc_start: 0.7389 (tp30) cc_final: 0.6959 (tp30) REVERT: A 910 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8162 (mtmm) REVERT: A 994 PHE cc_start: 0.8196 (m-80) cc_final: 0.7629 (m-80) REVERT: A 1014 LYS cc_start: 0.7529 (mtpp) cc_final: 0.7197 (mtpp) REVERT: A 1015 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6138 (mm-30) REVERT: A 1017 SER cc_start: 0.8465 (t) cc_final: 0.8178 (m) REVERT: A 1023 VAL cc_start: 0.8136 (t) cc_final: 0.7903 (t) REVERT: A 1032 GLN cc_start: 0.7250 (tp40) cc_final: 0.6864 (tp40) REVERT: A 1049 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 1063 GLU cc_start: 0.7226 (tt0) cc_final: 0.6928 (tt0) REVERT: A 1132 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7834 (mtmm) REVERT: A 1155 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7330 (ttmm) REVERT: A 1186 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8172 (p) REVERT: A 1189 ASP cc_start: 0.7504 (t0) cc_final: 0.7055 (t0) REVERT: A 1223 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: A 1306 LYS cc_start: 0.8235 (tptt) cc_final: 0.7747 (tptt) REVERT: A 1325 ASP cc_start: 0.7383 (m-30) cc_final: 0.7108 (m-30) REVERT: A 1345 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7129 (mtp180) REVERT: A 1348 SER cc_start: 0.8256 (m) cc_final: 0.7974 (p) REVERT: A 1351 ASP cc_start: 0.7281 (t0) cc_final: 0.6969 (t0) REVERT: A 1364 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: A 1379 GLU cc_start: 0.7083 (tt0) cc_final: 0.6854 (tt0) REVERT: A 1430 CYS cc_start: 0.8005 (p) cc_final: 0.7743 (p) REVERT: A 1455 SER cc_start: 0.8257 (p) cc_final: 0.7921 (m) REVERT: A 1479 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7381 (mtpp) REVERT: B 37 LYS cc_start: 0.7770 (mttm) cc_final: 0.7547 (mttm) REVERT: B 87 LYS cc_start: 0.7605 (tptt) cc_final: 0.7305 (tptm) REVERT: B 91 ILE cc_start: 0.8216 (pt) cc_final: 0.7981 (pt) REVERT: B 92 TYR cc_start: 0.7478 (m-80) cc_final: 0.6918 (m-80) REVERT: B 106 SER cc_start: 0.7800 (t) cc_final: 0.7269 (m) REVERT: B 192 LYS cc_start: 0.8351 (mmtp) cc_final: 0.8084 (mmtt) REVERT: B 254 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: B 282 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7060 (ttm-80) REVERT: B 320 PHE cc_start: 0.7781 (t80) cc_final: 0.7538 (t80) REVERT: B 340 LYS cc_start: 0.7763 (mttm) cc_final: 0.7346 (mttm) REVERT: B 345 LYS cc_start: 0.7653 (mmtp) cc_final: 0.7215 (mmtp) REVERT: B 348 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 358 GLU cc_start: 0.6770 (pm20) cc_final: 0.6461 (pm20) REVERT: B 380 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7251 (mmm-85) REVERT: B 413 LYS cc_start: 0.7865 (tttp) cc_final: 0.7533 (tttm) REVERT: B 432 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6953 (tm-30) REVERT: B 433 LEU cc_start: 0.8304 (mt) cc_final: 0.7399 (mt) REVERT: B 439 ILE cc_start: 0.8122 (mt) cc_final: 0.7798 (mp) REVERT: B 472 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7436 (mmt180) REVERT: B 497 LYS cc_start: 0.7964 (tptt) cc_final: 0.7699 (tptt) REVERT: B 510 CYS cc_start: 0.8360 (t) cc_final: 0.7639 (t) REVERT: B 578 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7857 (mmtp) REVERT: B 579 ASP cc_start: 0.7412 (t0) cc_final: 0.7121 (t0) REVERT: B 589 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7728 (ttpp) REVERT: B 590 LEU cc_start: 0.8390 (mt) cc_final: 0.8126 (mt) REVERT: B 629 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6697 (mm-30) REVERT: B 630 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7763 (mmtp) REVERT: B 637 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7140 (ttpt) REVERT: B 638 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7591 (mtm-85) REVERT: B 641 ASP cc_start: 0.7105 (m-30) cc_final: 0.6684 (m-30) REVERT: B 666 ASP cc_start: 0.6810 (p0) cc_final: 0.6553 (p0) REVERT: B 717 ASN cc_start: 0.7784 (m110) cc_final: 0.7568 (m-40) REVERT: B 788 TYR cc_start: 0.7720 (m-80) cc_final: 0.7205 (m-80) REVERT: B 958 CYS cc_start: 0.8612 (m) cc_final: 0.8369 (m) REVERT: B 1029 TYR cc_start: 0.8272 (m-80) cc_final: 0.8056 (m-10) REVERT: B 1052 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8361 (ptpt) REVERT: B 1108 PHE cc_start: 0.8353 (t80) cc_final: 0.8031 (t80) REVERT: C 81 LYS cc_start: 0.7955 (ptpp) cc_final: 0.7730 (ptpp) REVERT: C 97 CYS cc_start: 0.4920 (p) cc_final: 0.4604 (p) REVERT: C 100 GLU cc_start: 0.7250 (tt0) cc_final: 0.7035 (tt0) REVERT: C 104 ASP cc_start: 0.7705 (t0) cc_final: 0.7339 (t0) REVERT: C 113 ARG cc_start: 0.8067 (tpt90) cc_final: 0.7743 (tpt90) REVERT: C 121 ILE cc_start: 0.8166 (mm) cc_final: 0.7848 (mt) REVERT: C 152 LYS cc_start: 0.8591 (mttm) cc_final: 0.8371 (mttm) REVERT: C 185 GLU cc_start: 0.7201 (tt0) cc_final: 0.6917 (tt0) REVERT: C 221 ASP cc_start: 0.7847 (t0) cc_final: 0.7555 (t0) REVERT: E 35 GLN cc_start: 0.7868 (tt0) cc_final: 0.7522 (tt0) REVERT: E 64 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: E 79 GLU cc_start: 0.7337 (mp0) cc_final: 0.6876 (mp0) REVERT: E 86 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7709 (t) REVERT: E 129 GLN cc_start: 0.7280 (tt0) cc_final: 0.6441 (tt0) REVERT: E 132 GLN cc_start: 0.6960 (tt0) cc_final: 0.6730 (tt0) REVERT: E 155 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6920 (mt-10) REVERT: E 166 ARG cc_start: 0.7616 (mtm180) cc_final: 0.6912 (mtm180) REVERT: E 197 SER cc_start: 0.8327 (p) cc_final: 0.7948 (m) REVERT: E 205 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7802 (t) REVERT: F 107 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7653 (ttm170) REVERT: F 112 ASP cc_start: 0.8124 (p0) cc_final: 0.7863 (p0) REVERT: F 124 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7533 (mt) REVERT: G 131 MET cc_start: 0.0256 (mtp) cc_final: -0.0053 (mtp) REVERT: H 42 ASP cc_start: 0.7479 (m-30) cc_final: 0.7112 (m-30) REVERT: H 81 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5304 (ptt-90) REVERT: H 122 LEU cc_start: 0.8242 (mt) cc_final: 0.7660 (mt) REVERT: I 14 ILE cc_start: 0.8427 (mm) cc_final: 0.8151 (mm) REVERT: I 66 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (p) REVERT: I 110 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8334 (mt) REVERT: J 53 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7930 (m) REVERT: J 62 TYR cc_start: 0.8412 (m-80) cc_final: 0.8112 (m-80) REVERT: K 21 ILE cc_start: 0.8629 (mp) cc_final: 0.8385 (mt) REVERT: K 23 LYS cc_start: 0.7757 (tptp) cc_final: 0.7353 (tptp) REVERT: K 37 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7848 (mptt) REVERT: K 50 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7950 (mt) REVERT: K 52 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7879 (mmtp) REVERT: K 69 HIS cc_start: 0.7665 (m90) cc_final: 0.7394 (m90) REVERT: K 104 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7632 (mtt-85) REVERT: L 16 ILE cc_start: 0.8513 (mm) cc_final: 0.7858 (mm) REVERT: U 274 GLN cc_start: 0.0467 (OUTLIER) cc_final: -0.0144 (pp30) REVERT: U 287 LYS cc_start: 0.4294 (OUTLIER) cc_final: 0.3675 (tppp) REVERT: U 397 MET cc_start: 0.6643 (mtp) cc_final: 0.6272 (mtp) REVERT: U 408 GLU cc_start: 0.6288 (pp20) cc_final: 0.5689 (pp20) REVERT: U 510 LYS cc_start: 0.7093 (ptmm) cc_final: 0.6736 (ptmm) REVERT: U 555 ARG cc_start: 0.6778 (mtm110) cc_final: 0.6477 (mtm110) REVERT: U 598 LYS cc_start: 0.7524 (mttt) cc_final: 0.7143 (mttt) outliers start: 196 outliers final: 85 residues processed: 1149 average time/residue: 0.2375 time to fit residues: 418.5342 Evaluate side-chains 1044 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 937 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 104 ARG Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 78 PRO Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 164 GLN Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 174 LEU Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 376 ARG Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 740 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A1190 GLN A1194 ASN B 111 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN B1117 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 53 ASN I 84 HIS K 2 ASN K 76 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 GLN U 198 GLN U 230 GLN U 327 ASN U 513 GLN ** U 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 564 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115898 restraints weight = 62166.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120274 restraints weight = 29761.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120951 restraints weight = 17183.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122089 restraints weight = 12950.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122691 restraints weight = 10302.097| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36662 Z= 0.162 Angle : 0.632 12.146 49742 Z= 0.322 Chirality : 0.045 0.195 5565 Planarity : 0.005 0.062 6258 Dihedral : 12.908 179.925 5580 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.57 % Rotamer: Outliers : 4.79 % Allowed : 13.79 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4314 helix: 0.84 (0.13), residues: 1576 sheet: -0.59 (0.21), residues: 583 loop : -1.03 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1356 TYR 0.023 0.001 TYR A 859 PHE 0.022 0.002 PHE A 361 TRP 0.017 0.001 TRP B 27 HIS 0.009 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00365 (36629) covalent geometry : angle 0.62217 (49695) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.33975 ( 2) hydrogen bonds : bond 0.04372 ( 1505) hydrogen bonds : angle 5.21604 ( 4231) metal coordination : bond 0.00803 ( 32) metal coordination : angle 3.72054 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 942 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7060 (mtm-85) REVERT: A 110 VAL cc_start: 0.6784 (t) cc_final: 0.6327 (m) REVERT: A 133 SER cc_start: 0.7868 (m) cc_final: 0.7568 (p) REVERT: A 238 MET cc_start: 0.7972 (mtp) cc_final: 0.7658 (mtt) REVERT: A 308 LYS cc_start: 0.7407 (tttm) cc_final: 0.7177 (tttm) REVERT: A 319 ASP cc_start: 0.7643 (t0) cc_final: 0.7432 (t0) REVERT: A 340 LYS cc_start: 0.8136 (tttt) cc_final: 0.7683 (ttmt) REVERT: A 347 GLU cc_start: 0.6813 (mp0) cc_final: 0.6310 (mp0) REVERT: A 417 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7866 (mtpt) REVERT: A 430 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7318 (mtm180) REVERT: A 489 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7485 (p) REVERT: A 517 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6759 (mm-30) REVERT: A 539 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: A 561 MET cc_start: 0.7497 (mmt) cc_final: 0.7276 (mmt) REVERT: A 608 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 639 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 692 SER cc_start: 0.8242 (p) cc_final: 0.8024 (p) REVERT: A 697 LYS cc_start: 0.7911 (tptt) cc_final: 0.7598 (tptt) REVERT: A 701 ASP cc_start: 0.7231 (t70) cc_final: 0.6747 (t0) REVERT: A 711 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7441 (mm-40) REVERT: A 712 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: A 714 ILE cc_start: 0.8219 (mm) cc_final: 0.7959 (mt) REVERT: A 715 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6812 (tm-30) REVERT: A 818 GLU cc_start: 0.7258 (tp30) cc_final: 0.6866 (tp30) REVERT: A 910 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8175 (mtmm) REVERT: A 916 PHE cc_start: 0.7909 (t80) cc_final: 0.7631 (t80) REVERT: A 940 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7697 (mtmm) REVERT: A 967 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7614 (mtt180) REVERT: A 985 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7363 (ttp-110) REVERT: A 994 PHE cc_start: 0.8276 (m-80) cc_final: 0.7871 (m-80) REVERT: A 1011 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 1014 LYS cc_start: 0.7373 (mtpp) cc_final: 0.7156 (mtpp) REVERT: A 1015 GLU cc_start: 0.6411 (mm-30) cc_final: 0.6094 (mm-30) REVERT: A 1017 SER cc_start: 0.8312 (t) cc_final: 0.8063 (m) REVERT: A 1023 VAL cc_start: 0.8222 (t) cc_final: 0.7959 (t) REVERT: A 1032 GLN cc_start: 0.7304 (tp40) cc_final: 0.6986 (tp40) REVERT: A 1049 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 1063 GLU cc_start: 0.7148 (tt0) cc_final: 0.6847 (tt0) REVERT: A 1132 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8096 (mtmm) REVERT: A 1186 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 1189 ASP cc_start: 0.7775 (t0) cc_final: 0.7335 (t70) REVERT: A 1198 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 1223 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: A 1306 LYS cc_start: 0.8114 (tptt) cc_final: 0.7502 (tptt) REVERT: A 1325 ASP cc_start: 0.7212 (m-30) cc_final: 0.6998 (m-30) REVERT: A 1351 ASP cc_start: 0.7455 (t0) cc_final: 0.7102 (t0) REVERT: A 1361 ASP cc_start: 0.7115 (p0) cc_final: 0.6813 (p0) REVERT: A 1430 CYS cc_start: 0.7954 (p) cc_final: 0.7606 (p) REVERT: A 1440 MET cc_start: 0.8155 (mmt) cc_final: 0.7666 (mmt) REVERT: A 1441 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 1455 SER cc_start: 0.8130 (p) cc_final: 0.7822 (t) REVERT: A 1479 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7436 (mtpp) REVERT: B 37 LYS cc_start: 0.7798 (mttm) cc_final: 0.7590 (mttm) REVERT: B 92 TYR cc_start: 0.7398 (m-80) cc_final: 0.6911 (m-80) REVERT: B 106 SER cc_start: 0.7788 (t) cc_final: 0.7204 (m) REVERT: B 192 LYS cc_start: 0.8343 (mmtp) cc_final: 0.7994 (mmtt) REVERT: B 254 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: B 286 GLU cc_start: 0.6346 (mt-10) cc_final: 0.5849 (mt-10) REVERT: B 311 ILE cc_start: 0.8456 (mm) cc_final: 0.8208 (mt) REVERT: B 320 PHE cc_start: 0.7665 (t80) cc_final: 0.7142 (t80) REVERT: B 345 LYS cc_start: 0.7654 (mmtp) cc_final: 0.7201 (mmtp) REVERT: B 363 TYR cc_start: 0.7904 (m-80) cc_final: 0.7659 (m-80) REVERT: B 380 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7263 (mmt90) REVERT: B 388 TYR cc_start: 0.7988 (t80) cc_final: 0.7055 (t80) REVERT: B 403 LEU cc_start: 0.7777 (tp) cc_final: 0.7558 (mt) REVERT: B 413 LYS cc_start: 0.7779 (tttp) cc_final: 0.7434 (tttm) REVERT: B 432 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 433 LEU cc_start: 0.8395 (mt) cc_final: 0.7445 (mt) REVERT: B 438 ARG cc_start: 0.7029 (mmm160) cc_final: 0.6695 (mmm160) REVERT: B 497 LYS cc_start: 0.7897 (tptt) cc_final: 0.7503 (tptt) REVERT: B 510 CYS cc_start: 0.8258 (t) cc_final: 0.7549 (t) REVERT: B 584 MET cc_start: 0.7847 (mmm) cc_final: 0.7628 (mmm) REVERT: B 629 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6635 (mm-30) REVERT: B 630 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7737 (mmtp) REVERT: B 666 ASP cc_start: 0.7064 (p0) cc_final: 0.6670 (p0) REVERT: B 788 TYR cc_start: 0.7856 (m-80) cc_final: 0.7386 (m-80) REVERT: B 790 GLN cc_start: 0.7390 (mt0) cc_final: 0.7189 (mt0) REVERT: B 816 GLU cc_start: 0.7531 (tp30) cc_final: 0.7029 (tp30) REVERT: B 1029 TYR cc_start: 0.8327 (m-80) cc_final: 0.8085 (m-10) REVERT: B 1052 LYS cc_start: 0.8608 (ptmm) cc_final: 0.8377 (ptpt) REVERT: B 1108 PHE cc_start: 0.8333 (t80) cc_final: 0.7989 (t80) REVERT: C 97 CYS cc_start: 0.5452 (p) cc_final: 0.5169 (p) REVERT: C 104 ASP cc_start: 0.7629 (t0) cc_final: 0.7268 (t0) REVERT: C 121 ILE cc_start: 0.8312 (mm) cc_final: 0.8091 (mt) REVERT: C 152 LYS cc_start: 0.8650 (mttm) cc_final: 0.8398 (mttm) REVERT: C 221 ASP cc_start: 0.7779 (t0) cc_final: 0.7557 (t0) REVERT: C 228 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7634 (ttp80) REVERT: C 240 ARG cc_start: 0.7954 (ptp-110) cc_final: 0.7702 (mtp-110) REVERT: C 253 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7356 (ttmm) REVERT: E 18 MET cc_start: 0.8383 (mmt) cc_final: 0.8013 (mmt) REVERT: E 35 GLN cc_start: 0.7874 (tt0) cc_final: 0.7479 (tt0) REVERT: E 61 LEU cc_start: 0.8912 (tp) cc_final: 0.8645 (tt) REVERT: E 64 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7753 (t-90) REVERT: E 73 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6300 (t80) REVERT: E 79 GLU cc_start: 0.7365 (mp0) cc_final: 0.6841 (mp0) REVERT: E 86 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7798 (t) REVERT: E 155 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6869 (mt-10) REVERT: E 166 ARG cc_start: 0.7514 (mtm180) cc_final: 0.6739 (mtm180) REVERT: E 197 SER cc_start: 0.8508 (p) cc_final: 0.7902 (m) REVERT: E 205 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7752 (t) REVERT: F 112 ASP cc_start: 0.8057 (p0) cc_final: 0.7790 (p0) REVERT: F 124 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7582 (mt) REVERT: G 12 LEU cc_start: 0.7812 (mp) cc_final: 0.7575 (mm) REVERT: G 131 MET cc_start: -0.0545 (mtp) cc_final: -0.0954 (mtp) REVERT: G 137 ILE cc_start: 0.2528 (OUTLIER) cc_final: 0.2319 (mp) REVERT: H 42 ASP cc_start: 0.7533 (m-30) cc_final: 0.7101 (m-30) REVERT: H 52 LEU cc_start: 0.8794 (tp) cc_final: 0.8529 (tt) REVERT: H 122 LEU cc_start: 0.8242 (mt) cc_final: 0.7575 (mt) REVERT: H 124 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7591 (ttt-90) REVERT: I 46 GLN cc_start: 0.8027 (tt0) cc_final: 0.7505 (tm-30) REVERT: I 66 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8247 (p) REVERT: I 110 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8166 (mt) REVERT: J 53 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7883 (m) REVERT: J 62 TYR cc_start: 0.8283 (m-80) cc_final: 0.7938 (m-80) REVERT: K 17 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8323 (mtpt) REVERT: K 23 LYS cc_start: 0.7773 (tptp) cc_final: 0.7298 (tptp) REVERT: K 50 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7995 (mt) REVERT: K 52 LYS cc_start: 0.8267 (mmtp) cc_final: 0.8055 (mmtp) REVERT: K 69 HIS cc_start: 0.7533 (m90) cc_final: 0.7318 (m90) REVERT: U 183 LEU cc_start: 0.2397 (OUTLIER) cc_final: 0.1525 (mp) REVERT: U 225 LEU cc_start: 0.7034 (mt) cc_final: 0.6792 (mt) REVERT: U 274 GLN cc_start: 0.0141 (OUTLIER) cc_final: -0.0130 (pp30) REVERT: U 287 LYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3436 (tppp) REVERT: U 397 MET cc_start: 0.6660 (mtp) cc_final: 0.6148 (mtp) REVERT: U 408 GLU cc_start: 0.6565 (pp20) cc_final: 0.6140 (pp20) REVERT: U 510 LYS cc_start: 0.7732 (ptmm) cc_final: 0.7298 (ptmm) REVERT: U 555 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6522 (mtm110) REVERT: U 598 LYS cc_start: 0.7476 (mttt) cc_final: 0.7065 (mttt) outliers start: 183 outliers final: 107 residues processed: 1056 average time/residue: 0.2436 time to fit residues: 392.5533 Evaluate side-chains 1048 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 917 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 408 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 281 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 700 GLN A 704 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 76 GLN U 34 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114459 restraints weight = 56920.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117803 restraints weight = 27591.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119671 restraints weight = 15949.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120230 restraints weight = 11767.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120811 restraints weight = 9719.572| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 36662 Z= 0.314 Angle : 0.686 11.924 49742 Z= 0.349 Chirality : 0.049 0.214 5565 Planarity : 0.005 0.061 6258 Dihedral : 12.699 169.859 5519 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.52 % Favored : 93.27 % Rotamer: Outliers : 5.52 % Allowed : 15.70 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 4314 helix: 0.65 (0.13), residues: 1579 sheet: -0.77 (0.21), residues: 597 loop : -1.16 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 172 TYR 0.019 0.002 TYR J 43 PHE 0.034 0.002 PHE A 361 TRP 0.021 0.002 TRP B 27 HIS 0.012 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00714 (36629) covalent geometry : angle 0.67268 (49695) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.24482 ( 2) hydrogen bonds : bond 0.04669 ( 1505) hydrogen bonds : angle 5.19354 ( 4231) metal coordination : bond 0.01667 ( 32) metal coordination : angle 4.59632 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 943 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8161 (t) cc_final: 0.7709 (p) REVERT: A 30 GLU cc_start: 0.7388 (tt0) cc_final: 0.6408 (tt0) REVERT: A 33 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7120 (mtm110) REVERT: A 42 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7507 (mtmm) REVERT: A 70 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6880 (mtp85) REVERT: A 110 VAL cc_start: 0.6828 (t) cc_final: 0.6438 (m) REVERT: A 133 SER cc_start: 0.7928 (m) cc_final: 0.7549 (p) REVERT: A 319 ASP cc_start: 0.7767 (t0) cc_final: 0.7490 (t0) REVERT: A 340 LYS cc_start: 0.8234 (tttt) cc_final: 0.7801 (ttmt) REVERT: A 347 GLU cc_start: 0.6867 (mp0) cc_final: 0.6374 (mp0) REVERT: A 378 VAL cc_start: 0.8317 (t) cc_final: 0.8048 (p) REVERT: A 417 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7938 (mtpt) REVERT: A 428 ASP cc_start: 0.7547 (t70) cc_final: 0.7204 (t70) REVERT: A 430 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7374 (mtm180) REVERT: A 540 ASP cc_start: 0.7489 (m-30) cc_final: 0.6993 (m-30) REVERT: A 608 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 697 LYS cc_start: 0.7955 (tptt) cc_final: 0.7688 (tptt) REVERT: A 715 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 818 GLU cc_start: 0.7323 (tp30) cc_final: 0.6838 (tp30) REVERT: A 910 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8240 (mtmm) REVERT: A 922 PHE cc_start: 0.8563 (t80) cc_final: 0.8339 (t80) REVERT: A 931 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6791 (mtp85) REVERT: A 936 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6625 (tp30) REVERT: A 940 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7676 (mtmm) REVERT: A 985 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7229 (ttm170) REVERT: A 994 PHE cc_start: 0.8308 (m-80) cc_final: 0.7861 (m-80) REVERT: A 1014 LYS cc_start: 0.7361 (mtpp) cc_final: 0.7146 (mtpp) REVERT: A 1015 GLU cc_start: 0.6415 (mm-30) cc_final: 0.6092 (mm-30) REVERT: A 1017 SER cc_start: 0.8371 (t) cc_final: 0.8141 (m) REVERT: A 1032 GLN cc_start: 0.7331 (tp40) cc_final: 0.7024 (tp40) REVERT: A 1049 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 1063 GLU cc_start: 0.7236 (tt0) cc_final: 0.6918 (tt0) REVERT: A 1132 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8074 (mtmm) REVERT: A 1186 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 1189 ASP cc_start: 0.7836 (t0) cc_final: 0.7363 (t70) REVERT: A 1218 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8047 (tpp80) REVERT: A 1223 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6573 (m-30) REVERT: A 1306 LYS cc_start: 0.8146 (tptt) cc_final: 0.7505 (tptt) REVERT: A 1325 ASP cc_start: 0.7329 (m-30) cc_final: 0.7125 (m-30) REVERT: A 1351 ASP cc_start: 0.7384 (t0) cc_final: 0.7025 (t0) REVERT: A 1361 ASP cc_start: 0.7188 (p0) cc_final: 0.6852 (p0) REVERT: A 1455 SER cc_start: 0.8189 (p) cc_final: 0.7866 (t) REVERT: A 1479 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7444 (mtpp) REVERT: B 37 LYS cc_start: 0.7829 (mttm) cc_final: 0.7606 (mttm) REVERT: B 92 TYR cc_start: 0.7552 (m-80) cc_final: 0.7139 (m-80) REVERT: B 106 SER cc_start: 0.7831 (t) cc_final: 0.7292 (m) REVERT: B 192 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8104 (mmtt) REVERT: B 286 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5988 (mt-10) REVERT: B 320 PHE cc_start: 0.7690 (t80) cc_final: 0.7199 (t80) REVERT: B 324 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6727 (mtt-85) REVERT: B 340 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7933 (mmmt) REVERT: B 345 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7186 (mmtp) REVERT: B 363 TYR cc_start: 0.7895 (m-80) cc_final: 0.7689 (m-80) REVERT: B 380 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7270 (mmt90) REVERT: B 413 LYS cc_start: 0.7890 (tttp) cc_final: 0.7546 (tttm) REVERT: B 432 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7112 (tm-30) REVERT: B 433 LEU cc_start: 0.8421 (mt) cc_final: 0.7784 (mt) REVERT: B 438 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6654 (mmm160) REVERT: B 497 LYS cc_start: 0.7858 (tptt) cc_final: 0.7415 (tptt) REVERT: B 510 CYS cc_start: 0.8287 (t) cc_final: 0.7655 (t) REVERT: B 581 GLU cc_start: 0.7269 (tt0) cc_final: 0.7054 (tt0) REVERT: B 629 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6664 (mm-30) REVERT: B 630 LYS cc_start: 0.8045 (mmtp) cc_final: 0.7778 (mmtp) REVERT: B 666 ASP cc_start: 0.7001 (p0) cc_final: 0.6577 (p0) REVERT: B 788 TYR cc_start: 0.7846 (m-80) cc_final: 0.7513 (m-80) REVERT: B 816 GLU cc_start: 0.7575 (tp30) cc_final: 0.7133 (tp30) REVERT: B 1052 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8441 (ptpt) REVERT: B 1108 PHE cc_start: 0.8500 (t80) cc_final: 0.8119 (t80) REVERT: B 1112 ASP cc_start: 0.7330 (p0) cc_final: 0.7116 (p0) REVERT: C 30 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (t) REVERT: C 97 CYS cc_start: 0.5194 (p) cc_final: 0.4845 (p) REVERT: C 104 ASP cc_start: 0.7641 (t0) cc_final: 0.7216 (t0) REVERT: C 121 ILE cc_start: 0.8377 (mm) cc_final: 0.8139 (mt) REVERT: C 152 LYS cc_start: 0.8669 (mttm) cc_final: 0.8412 (mttm) REVERT: C 221 ASP cc_start: 0.7817 (t0) cc_final: 0.7578 (t0) REVERT: C 229 PHE cc_start: 0.8563 (m-80) cc_final: 0.8256 (m-80) REVERT: C 240 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7703 (mtp85) REVERT: C 253 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7376 (ttmm) REVERT: E 18 MET cc_start: 0.8361 (mmt) cc_final: 0.7986 (mmt) REVERT: E 35 GLN cc_start: 0.7959 (tt0) cc_final: 0.7627 (tt0) REVERT: E 64 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: E 73 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6481 (t80) REVERT: E 79 GLU cc_start: 0.7410 (mp0) cc_final: 0.6870 (mp0) REVERT: E 86 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7829 (t) REVERT: E 106 VAL cc_start: 0.8290 (t) cc_final: 0.7939 (p) REVERT: E 155 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6824 (mt-10) REVERT: E 166 ARG cc_start: 0.7670 (mtm180) cc_final: 0.6834 (mtm180) REVERT: E 197 SER cc_start: 0.8504 (p) cc_final: 0.7972 (m) REVERT: E 205 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7753 (t) REVERT: F 124 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7482 (mt) REVERT: G 131 MET cc_start: -0.0066 (mtp) cc_final: -0.0451 (mtp) REVERT: G 137 ILE cc_start: 0.2731 (OUTLIER) cc_final: 0.2524 (mp) REVERT: H 42 ASP cc_start: 0.7604 (m-30) cc_final: 0.7192 (m-30) REVERT: H 54 ASP cc_start: 0.8406 (p0) cc_final: 0.8084 (p0) REVERT: H 64 LEU cc_start: 0.8106 (mt) cc_final: 0.7753 (mt) REVERT: H 122 LEU cc_start: 0.8226 (mt) cc_final: 0.7576 (mt) REVERT: I 14 ILE cc_start: 0.8544 (mm) cc_final: 0.7799 (mm) REVERT: I 74 GLN cc_start: 0.7676 (pt0) cc_final: 0.7280 (pt0) REVERT: I 110 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8245 (mt) REVERT: J 53 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7866 (m) REVERT: J 62 TYR cc_start: 0.8282 (m-80) cc_final: 0.7986 (m-80) REVERT: K 17 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8395 (mtpp) REVERT: K 23 LYS cc_start: 0.7807 (tptp) cc_final: 0.7319 (tptp) REVERT: K 50 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8009 (mt) REVERT: K 52 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7949 (mmtp) REVERT: K 67 LEU cc_start: 0.8293 (mt) cc_final: 0.8028 (mm) REVERT: L 54 VAL cc_start: 0.8656 (t) cc_final: 0.8297 (m) REVERT: U 225 LEU cc_start: 0.7029 (mt) cc_final: 0.6776 (mt) REVERT: U 244 ASP cc_start: 0.8258 (m-30) cc_final: 0.8043 (m-30) REVERT: U 274 GLN cc_start: 0.0563 (OUTLIER) cc_final: 0.0241 (pp30) REVERT: U 287 LYS cc_start: 0.4200 (OUTLIER) cc_final: 0.3501 (tppp) REVERT: U 397 MET cc_start: 0.6695 (mtp) cc_final: 0.6158 (mtp) REVERT: U 416 ILE cc_start: 0.6089 (tp) cc_final: 0.5848 (tp) REVERT: U 510 LYS cc_start: 0.7699 (ptmm) cc_final: 0.7312 (ptmm) REVERT: U 555 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6485 (mtm110) REVERT: U 598 LYS cc_start: 0.7495 (mttt) cc_final: 0.7076 (mttt) outliers start: 211 outliers final: 140 residues processed: 1064 average time/residue: 0.2481 time to fit residues: 405.2016 Evaluate side-chains 1082 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 924 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 584 GLU Chi-restraints excluded: chain U residue 596 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 333 optimal weight: 20.0000 chunk 117 optimal weight: 0.0770 chunk 223 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 673 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN K 2 ASN K 76 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 552 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115021 restraints weight = 67277.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117643 restraints weight = 35813.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119006 restraints weight = 21629.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119808 restraints weight = 15462.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120028 restraints weight = 12824.305| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36662 Z= 0.173 Angle : 0.627 13.216 49742 Z= 0.316 Chirality : 0.045 0.207 5565 Planarity : 0.005 0.059 6258 Dihedral : 12.541 160.516 5512 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.03 % Favored : 93.76 % Rotamer: Outliers : 5.15 % Allowed : 17.09 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.13), residues: 4314 helix: 0.86 (0.13), residues: 1583 sheet: -0.66 (0.21), residues: 588 loop : -1.12 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 172 TYR 0.016 0.001 TYR A 859 PHE 0.027 0.002 PHE A 361 TRP 0.017 0.001 TRP B 27 HIS 0.012 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00396 (36629) covalent geometry : angle 0.61179 (49695) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.30291 ( 2) hydrogen bonds : bond 0.03944 ( 1505) hydrogen bonds : angle 4.97194 ( 4231) metal coordination : bond 0.00932 ( 32) metal coordination : angle 4.61689 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 931 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8160 (t) cc_final: 0.7752 (p) REVERT: A 30 GLU cc_start: 0.7234 (tt0) cc_final: 0.6541 (tt0) REVERT: A 33 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7367 (mtm110) REVERT: A 70 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6935 (mtp85) REVERT: A 104 MET cc_start: 0.7955 (mtp) cc_final: 0.7736 (mtp) REVERT: A 108 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7291 (mtm-85) REVERT: A 110 VAL cc_start: 0.6690 (t) cc_final: 0.6290 (m) REVERT: A 116 LYS cc_start: 0.7448 (mttm) cc_final: 0.7228 (mttm) REVERT: A 133 SER cc_start: 0.7934 (m) cc_final: 0.7583 (p) REVERT: A 238 MET cc_start: 0.7992 (mtp) cc_final: 0.7675 (mtt) REVERT: A 319 ASP cc_start: 0.7788 (t0) cc_final: 0.7414 (t0) REVERT: A 340 LYS cc_start: 0.8161 (tttt) cc_final: 0.7751 (ttmt) REVERT: A 347 GLU cc_start: 0.6766 (mp0) cc_final: 0.6264 (mp0) REVERT: A 417 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7888 (mtpt) REVERT: A 428 ASP cc_start: 0.7416 (t0) cc_final: 0.7142 (t70) REVERT: A 489 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 540 ASP cc_start: 0.7140 (m-30) cc_final: 0.6670 (m-30) REVERT: A 573 LYS cc_start: 0.6636 (mmtt) cc_final: 0.6383 (mmtm) REVERT: A 608 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7737 (t) REVERT: A 691 ASP cc_start: 0.6681 (m-30) cc_final: 0.6427 (m-30) REVERT: A 697 LYS cc_start: 0.7833 (tptt) cc_final: 0.7619 (tptt) REVERT: A 701 ASP cc_start: 0.7202 (t70) cc_final: 0.6723 (t0) REVERT: A 711 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7311 (mm-40) REVERT: A 769 MET cc_start: 0.8198 (mtp) cc_final: 0.7996 (mtp) REVERT: A 777 SER cc_start: 0.8730 (p) cc_final: 0.8382 (m) REVERT: A 818 GLU cc_start: 0.7229 (tp30) cc_final: 0.6716 (tp30) REVERT: A 910 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8125 (mtmm) REVERT: A 940 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7607 (mtmm) REVERT: A 985 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7250 (ttp80) REVERT: A 1017 SER cc_start: 0.8302 (t) cc_final: 0.8062 (m) REVERT: A 1023 VAL cc_start: 0.8313 (t) cc_final: 0.8080 (t) REVERT: A 1032 GLN cc_start: 0.7306 (tp40) cc_final: 0.7075 (tp40) REVERT: A 1049 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 1063 GLU cc_start: 0.7079 (tt0) cc_final: 0.6790 (tt0) REVERT: A 1132 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8036 (mtmm) REVERT: A 1160 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.7007 (ttm-80) REVERT: A 1189 ASP cc_start: 0.7716 (t0) cc_final: 0.7265 (t70) REVERT: A 1211 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7175 (tt) REVERT: A 1218 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.8187 (tpp80) REVERT: A 1223 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6478 (m-30) REVERT: A 1306 LYS cc_start: 0.8090 (tptt) cc_final: 0.7436 (tptt) REVERT: A 1339 ASP cc_start: 0.7086 (t0) cc_final: 0.6883 (t0) REVERT: A 1351 ASP cc_start: 0.7343 (t0) cc_final: 0.6962 (t0) REVERT: A 1361 ASP cc_start: 0.7168 (p0) cc_final: 0.6836 (p0) REVERT: A 1455 SER cc_start: 0.8277 (p) cc_final: 0.7881 (t) REVERT: A 1479 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7412 (mtpp) REVERT: B 92 TYR cc_start: 0.7446 (m-80) cc_final: 0.7156 (m-80) REVERT: B 106 SER cc_start: 0.7792 (t) cc_final: 0.7238 (m) REVERT: B 254 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6388 (mp-120) REVERT: B 286 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5863 (mt-10) REVERT: B 289 ILE cc_start: 0.8311 (mt) cc_final: 0.7982 (tt) REVERT: B 298 MET cc_start: 0.6893 (mtm) cc_final: 0.6685 (mtp) REVERT: B 320 PHE cc_start: 0.7615 (t80) cc_final: 0.7117 (t80) REVERT: B 324 ARG cc_start: 0.7093 (mtt-85) cc_final: 0.6784 (mtt-85) REVERT: B 340 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7830 (mmmt) REVERT: B 345 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7185 (mmtp) REVERT: B 363 TYR cc_start: 0.7885 (m-80) cc_final: 0.7631 (m-80) REVERT: B 413 LYS cc_start: 0.7829 (tttp) cc_final: 0.7502 (tttm) REVERT: B 432 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 433 LEU cc_start: 0.8443 (mt) cc_final: 0.7583 (mt) REVERT: B 438 ARG cc_start: 0.7032 (mmm160) cc_final: 0.6624 (mmm160) REVERT: B 497 LYS cc_start: 0.7770 (tptt) cc_final: 0.7478 (tptt) REVERT: B 510 CYS cc_start: 0.8270 (t) cc_final: 0.7550 (t) REVERT: B 629 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6603 (mm-30) REVERT: B 630 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7703 (mmtp) REVERT: B 666 ASP cc_start: 0.6933 (p0) cc_final: 0.6600 (p0) REVERT: B 785 TYR cc_start: 0.7843 (t80) cc_final: 0.7302 (t80) REVERT: B 788 TYR cc_start: 0.7811 (m-80) cc_final: 0.7491 (m-80) REVERT: B 905 ASP cc_start: 0.6689 (t0) cc_final: 0.6412 (t0) REVERT: B 1029 TYR cc_start: 0.8281 (m-80) cc_final: 0.8072 (m-10) REVERT: B 1052 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8411 (ptpt) REVERT: B 1108 PHE cc_start: 0.8419 (t80) cc_final: 0.8087 (t80) REVERT: B 1112 ASP cc_start: 0.7304 (p0) cc_final: 0.7015 (p0) REVERT: C 41 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (mm-30) REVERT: C 97 CYS cc_start: 0.5418 (p) cc_final: 0.5181 (p) REVERT: C 104 ASP cc_start: 0.7543 (t0) cc_final: 0.7134 (t0) REVERT: C 121 ILE cc_start: 0.8357 (mm) cc_final: 0.8125 (mt) REVERT: C 152 LYS cc_start: 0.8688 (mttm) cc_final: 0.8419 (mttm) REVERT: C 185 GLU cc_start: 0.7149 (tt0) cc_final: 0.6884 (tt0) REVERT: C 229 PHE cc_start: 0.8483 (m-80) cc_final: 0.8177 (m-80) REVERT: C 253 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7403 (ttmm) REVERT: E 18 MET cc_start: 0.8320 (mmt) cc_final: 0.7970 (mmt) REVERT: E 35 GLN cc_start: 0.7896 (tt0) cc_final: 0.7549 (tt0) REVERT: E 61 LEU cc_start: 0.8918 (tp) cc_final: 0.8638 (tt) REVERT: E 64 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7765 (t-90) REVERT: E 73 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6602 (t80) REVERT: E 79 GLU cc_start: 0.7313 (mp0) cc_final: 0.6819 (mp0) REVERT: E 86 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7739 (t) REVERT: E 106 VAL cc_start: 0.8273 (t) cc_final: 0.7950 (p) REVERT: E 155 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6805 (mt-10) REVERT: E 166 ARG cc_start: 0.7568 (mtm180) cc_final: 0.6858 (mtm180) REVERT: E 197 SER cc_start: 0.8529 (p) cc_final: 0.7920 (m) REVERT: E 205 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7774 (t) REVERT: F 112 ASP cc_start: 0.8162 (p0) cc_final: 0.7871 (p0) REVERT: F 124 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7590 (mt) REVERT: G 131 MET cc_start: -0.0012 (mtp) cc_final: -0.0402 (mtp) REVERT: G 137 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.2319 (mp) REVERT: H 42 ASP cc_start: 0.7495 (m-30) cc_final: 0.7106 (m-30) REVERT: H 52 LEU cc_start: 0.8689 (tp) cc_final: 0.8276 (tt) REVERT: H 64 LEU cc_start: 0.8178 (mt) cc_final: 0.7780 (mt) REVERT: H 122 LEU cc_start: 0.8200 (mt) cc_final: 0.7535 (mt) REVERT: H 124 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7667 (ttt-90) REVERT: I 74 GLN cc_start: 0.7641 (pt0) cc_final: 0.7251 (pt0) REVERT: I 110 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8251 (mt) REVERT: J 53 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7896 (m) REVERT: J 62 TYR cc_start: 0.8276 (m-80) cc_final: 0.7955 (m-80) REVERT: K 23 LYS cc_start: 0.7749 (tptp) cc_final: 0.7293 (tptp) REVERT: K 50 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8023 (mt) REVERT: K 52 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7850 (mmtp) REVERT: L 54 VAL cc_start: 0.8642 (t) cc_final: 0.8216 (m) REVERT: U 225 LEU cc_start: 0.7054 (mt) cc_final: 0.6825 (mt) REVERT: U 243 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7417 (tmtt) REVERT: U 287 LYS cc_start: 0.4271 (OUTLIER) cc_final: 0.3654 (tppp) REVERT: U 397 MET cc_start: 0.6771 (mtp) cc_final: 0.6236 (mtp) REVERT: U 416 ILE cc_start: 0.6064 (tp) cc_final: 0.5803 (tp) REVERT: U 510 LYS cc_start: 0.7645 (ptmm) cc_final: 0.7193 (ptmm) REVERT: U 541 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.5769 (ptt180) REVERT: U 550 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6780 (mtp180) REVERT: U 555 ARG cc_start: 0.6981 (mtm110) cc_final: 0.6420 (mtm110) REVERT: U 598 LYS cc_start: 0.7464 (mttt) cc_final: 0.7054 (mttt) outliers start: 197 outliers final: 135 residues processed: 1043 average time/residue: 0.2477 time to fit residues: 396.8657 Evaluate side-chains 1067 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 914 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 541 ARG Chi-restraints excluded: chain U residue 584 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 278 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 740 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN E 107 GLN E 132 GLN K 2 ASN K 76 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116885 restraints weight = 59710.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120542 restraints weight = 27201.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120925 restraints weight = 16292.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122015 restraints weight = 13527.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123212 restraints weight = 10358.276| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36662 Z= 0.164 Angle : 0.615 10.041 49742 Z= 0.310 Chirality : 0.045 0.261 5565 Planarity : 0.005 0.059 6258 Dihedral : 12.383 162.388 5504 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 5.23 % Allowed : 17.56 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.13), residues: 4314 helix: 0.95 (0.13), residues: 1584 sheet: -0.65 (0.21), residues: 582 loop : -1.10 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 172 TYR 0.014 0.001 TYR B 262 PHE 0.017 0.002 PHE C 38 TRP 0.017 0.001 TRP B 27 HIS 0.008 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00376 (36629) covalent geometry : angle 0.60443 (49695) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.27655 ( 2) hydrogen bonds : bond 0.03808 ( 1505) hydrogen bonds : angle 4.84138 ( 4231) metal coordination : bond 0.00847 ( 32) metal coordination : angle 3.86382 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 909 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8151 (t) cc_final: 0.7754 (p) REVERT: A 30 GLU cc_start: 0.7311 (tt0) cc_final: 0.6575 (tt0) REVERT: A 33 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7305 (mtm110) REVERT: A 70 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7084 (mtp85) REVERT: A 104 MET cc_start: 0.7905 (mtp) cc_final: 0.7668 (mtp) REVERT: A 108 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7358 (mtm-85) REVERT: A 110 VAL cc_start: 0.6636 (t) cc_final: 0.6268 (m) REVERT: A 116 LYS cc_start: 0.7420 (mttm) cc_final: 0.7198 (mttm) REVERT: A 133 SER cc_start: 0.7937 (m) cc_final: 0.7588 (p) REVERT: A 238 MET cc_start: 0.8034 (mtp) cc_final: 0.7634 (mtm) REVERT: A 319 ASP cc_start: 0.7777 (t0) cc_final: 0.7433 (t0) REVERT: A 340 LYS cc_start: 0.8217 (tttt) cc_final: 0.7770 (ttmt) REVERT: A 347 GLU cc_start: 0.6825 (mp0) cc_final: 0.6383 (mp0) REVERT: A 417 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7909 (mtpt) REVERT: A 428 ASP cc_start: 0.7454 (t0) cc_final: 0.7115 (t70) REVERT: A 489 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7553 (p) REVERT: A 540 ASP cc_start: 0.7203 (m-30) cc_final: 0.6919 (m-30) REVERT: A 573 LYS cc_start: 0.6750 (mmtt) cc_final: 0.6500 (mmtm) REVERT: A 608 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7770 (t) REVERT: A 691 ASP cc_start: 0.6731 (m-30) cc_final: 0.6478 (m-30) REVERT: A 697 LYS cc_start: 0.7870 (tptt) cc_final: 0.7603 (tptt) REVERT: A 701 ASP cc_start: 0.7239 (t70) cc_final: 0.6741 (t0) REVERT: A 711 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7340 (mm-40) REVERT: A 818 GLU cc_start: 0.7292 (tp30) cc_final: 0.6772 (tp30) REVERT: A 910 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8104 (mtmm) REVERT: A 916 PHE cc_start: 0.7875 (t80) cc_final: 0.7649 (t80) REVERT: A 931 ARG cc_start: 0.7362 (mtp85) cc_final: 0.7058 (mtt-85) REVERT: A 936 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6873 (tp30) REVERT: A 940 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7666 (mtmm) REVERT: A 1015 GLU cc_start: 0.6284 (mm-30) cc_final: 0.6019 (mm-30) REVERT: A 1023 VAL cc_start: 0.8286 (t) cc_final: 0.8025 (t) REVERT: A 1032 GLN cc_start: 0.7314 (tp40) cc_final: 0.7071 (tp40) REVERT: A 1078 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7555 (mm-40) REVERT: A 1132 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8069 (mtmm) REVERT: A 1160 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.7039 (ttm-80) REVERT: A 1189 ASP cc_start: 0.7508 (t0) cc_final: 0.7179 (t70) REVERT: A 1218 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8104 (tpp80) REVERT: A 1223 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: A 1306 LYS cc_start: 0.8047 (tptt) cc_final: 0.7334 (tptt) REVERT: A 1339 ASP cc_start: 0.7240 (t0) cc_final: 0.7009 (t0) REVERT: A 1351 ASP cc_start: 0.7413 (t0) cc_final: 0.7001 (t0) REVERT: A 1356 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6891 (mtp85) REVERT: A 1361 ASP cc_start: 0.7147 (p0) cc_final: 0.6786 (p0) REVERT: A 1449 ASP cc_start: 0.7876 (t0) cc_final: 0.7545 (t0) REVERT: A 1455 SER cc_start: 0.8198 (p) cc_final: 0.7734 (t) REVERT: A 1472 ASP cc_start: 0.7610 (m-30) cc_final: 0.7383 (m-30) REVERT: A 1479 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7460 (mtpp) REVERT: B 92 TYR cc_start: 0.7474 (m-80) cc_final: 0.7207 (m-80) REVERT: B 106 SER cc_start: 0.7749 (t) cc_final: 0.7184 (m) REVERT: B 254 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6320 (mp-120) REVERT: B 286 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5925 (mt-10) REVERT: B 320 PHE cc_start: 0.7666 (t80) cc_final: 0.7449 (t80) REVERT: B 340 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7914 (mmmt) REVERT: B 345 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7250 (mmtp) REVERT: B 363 TYR cc_start: 0.7853 (m-80) cc_final: 0.7558 (m-80) REVERT: B 388 TYR cc_start: 0.7950 (t80) cc_final: 0.7152 (t80) REVERT: B 413 LYS cc_start: 0.7756 (tttp) cc_final: 0.7425 (tttm) REVERT: B 432 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 433 LEU cc_start: 0.8388 (mt) cc_final: 0.7716 (mt) REVERT: B 438 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6588 (mmm160) REVERT: B 497 LYS cc_start: 0.7738 (tptt) cc_final: 0.7461 (tptt) REVERT: B 510 CYS cc_start: 0.8264 (t) cc_final: 0.7593 (t) REVERT: B 581 GLU cc_start: 0.7269 (tt0) cc_final: 0.6910 (tt0) REVERT: B 629 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6664 (mm-30) REVERT: B 630 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7733 (mmtp) REVERT: B 637 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7895 (ttmm) REVERT: B 666 ASP cc_start: 0.6999 (p0) cc_final: 0.6652 (p0) REVERT: B 785 TYR cc_start: 0.7833 (t80) cc_final: 0.7346 (t80) REVERT: B 788 TYR cc_start: 0.7819 (m-80) cc_final: 0.7473 (m-80) REVERT: B 816 GLU cc_start: 0.7527 (tp30) cc_final: 0.6903 (tp30) REVERT: B 905 ASP cc_start: 0.6746 (t0) cc_final: 0.6511 (t0) REVERT: B 917 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8284 (ttmm) REVERT: B 1029 TYR cc_start: 0.8304 (m-80) cc_final: 0.8002 (m-10) REVERT: B 1052 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8437 (ptpt) REVERT: B 1060 HIS cc_start: 0.7722 (t70) cc_final: 0.7479 (t70) REVERT: B 1108 PHE cc_start: 0.8432 (t80) cc_final: 0.8050 (t80) REVERT: C 30 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7736 (t) REVERT: C 41 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6955 (mm-30) REVERT: C 59 LEU cc_start: 0.7816 (mt) cc_final: 0.7567 (mp) REVERT: C 86 ARG cc_start: 0.6694 (ptt180) cc_final: 0.6490 (ptt180) REVERT: C 97 CYS cc_start: 0.5315 (p) cc_final: 0.5046 (p) REVERT: C 104 ASP cc_start: 0.7609 (t0) cc_final: 0.7205 (t0) REVERT: C 121 ILE cc_start: 0.8324 (mm) cc_final: 0.8097 (mt) REVERT: C 152 LYS cc_start: 0.8654 (mttm) cc_final: 0.8391 (mttm) REVERT: C 221 ASP cc_start: 0.7860 (t0) cc_final: 0.7634 (t70) REVERT: C 253 LYS cc_start: 0.7630 (ttmm) cc_final: 0.7380 (ttmm) REVERT: E 18 MET cc_start: 0.8348 (mmt) cc_final: 0.7968 (mmt) REVERT: E 35 GLN cc_start: 0.7877 (tt0) cc_final: 0.7634 (tt0) REVERT: E 61 LEU cc_start: 0.8869 (tp) cc_final: 0.8621 (tt) REVERT: E 64 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: E 73 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6595 (t80) REVERT: E 79 GLU cc_start: 0.7300 (mp0) cc_final: 0.6802 (mp0) REVERT: E 86 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7814 (t) REVERT: E 155 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6885 (mt-10) REVERT: E 166 ARG cc_start: 0.7561 (mtm180) cc_final: 0.6789 (mtm180) REVERT: E 197 SER cc_start: 0.8494 (p) cc_final: 0.7972 (m) REVERT: F 124 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7629 (mt) REVERT: G 131 MET cc_start: -0.0247 (mtp) cc_final: -0.0607 (mtp) REVERT: G 137 ILE cc_start: 0.2515 (OUTLIER) cc_final: 0.2225 (mp) REVERT: H 7 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6559 (tm-30) REVERT: H 42 ASP cc_start: 0.7615 (m-30) cc_final: 0.7200 (m-30) REVERT: H 52 LEU cc_start: 0.8657 (tp) cc_final: 0.8263 (tt) REVERT: H 64 LEU cc_start: 0.8139 (mt) cc_final: 0.7744 (mt) REVERT: H 122 LEU cc_start: 0.8216 (mt) cc_final: 0.7568 (mt) REVERT: H 124 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7618 (ttt-90) REVERT: I 14 ILE cc_start: 0.8416 (mm) cc_final: 0.8208 (mm) REVERT: I 46 GLN cc_start: 0.8007 (tt0) cc_final: 0.7480 (tm-30) REVERT: I 74 GLN cc_start: 0.7488 (pt0) cc_final: 0.7195 (pt0) REVERT: I 110 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8221 (mt) REVERT: J 53 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7853 (m) REVERT: J 62 TYR cc_start: 0.8155 (m-80) cc_final: 0.7860 (m-80) REVERT: K 17 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8259 (mtpp) REVERT: K 23 LYS cc_start: 0.7748 (tptp) cc_final: 0.7241 (tptp) REVERT: K 50 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7975 (mt) REVERT: K 52 LYS cc_start: 0.8322 (mmtp) cc_final: 0.7907 (mmtp) REVERT: L 54 VAL cc_start: 0.8692 (t) cc_final: 0.8250 (m) REVERT: U 225 LEU cc_start: 0.7088 (mt) cc_final: 0.6860 (mt) REVERT: U 287 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.3512 (tppp) REVERT: U 397 MET cc_start: 0.6748 (mtp) cc_final: 0.6195 (mtp) REVERT: U 416 ILE cc_start: 0.6062 (tp) cc_final: 0.5805 (tp) REVERT: U 510 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7151 (ptmm) REVERT: U 541 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5658 (ptt180) REVERT: U 550 ARG cc_start: 0.6988 (mtp180) cc_final: 0.6745 (mtp180) REVERT: U 555 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6354 (mtm110) REVERT: U 598 LYS cc_start: 0.7495 (mttt) cc_final: 0.7077 (mttt) outliers start: 200 outliers final: 142 residues processed: 1023 average time/residue: 0.2621 time to fit residues: 408.9620 Evaluate side-chains 1048 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 889 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 541 ARG Chi-restraints excluded: chain U residue 584 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 298 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 413 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 722 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN K 2 ASN K 36 ASN K 76 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116791 restraints weight = 56714.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120455 restraints weight = 26335.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120771 restraints weight = 15042.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121967 restraints weight = 13142.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122577 restraints weight = 9767.128| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 36662 Z= 0.202 Angle : 0.633 13.467 49742 Z= 0.319 Chirality : 0.046 0.260 5565 Planarity : 0.005 0.058 6258 Dihedral : 12.353 164.146 5500 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.40 % Favored : 93.39 % Rotamer: Outliers : 5.52 % Allowed : 18.05 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4314 helix: 0.94 (0.13), residues: 1588 sheet: -0.62 (0.21), residues: 576 loop : -1.13 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 172 TYR 0.018 0.001 TYR B 262 PHE 0.020 0.002 PHE C 38 TRP 0.018 0.002 TRP B 27 HIS 0.007 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00464 (36629) covalent geometry : angle 0.62180 (49695) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.23155 ( 2) hydrogen bonds : bond 0.03875 ( 1505) hydrogen bonds : angle 4.83087 ( 4231) metal coordination : bond 0.01107 ( 32) metal coordination : angle 3.97676 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 910 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8147 (t) cc_final: 0.7738 (p) REVERT: A 30 GLU cc_start: 0.7322 (tt0) cc_final: 0.7048 (tt0) REVERT: A 70 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7150 (mtp85) REVERT: A 104 MET cc_start: 0.7960 (mtp) cc_final: 0.7702 (mtp) REVERT: A 108 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7381 (mtm-85) REVERT: A 116 LYS cc_start: 0.7433 (mttm) cc_final: 0.7200 (mttm) REVERT: A 133 SER cc_start: 0.7946 (m) cc_final: 0.7592 (p) REVERT: A 238 MET cc_start: 0.8089 (mtp) cc_final: 0.7659 (mtm) REVERT: A 340 LYS cc_start: 0.8229 (tttt) cc_final: 0.8029 (ttmt) REVERT: A 347 GLU cc_start: 0.6837 (mp0) cc_final: 0.6403 (mp0) REVERT: A 417 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7921 (mtpt) REVERT: A 428 ASP cc_start: 0.7540 (t0) cc_final: 0.7174 (t70) REVERT: A 489 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 540 ASP cc_start: 0.7315 (m-30) cc_final: 0.7026 (m-30) REVERT: A 573 LYS cc_start: 0.6775 (mmtt) cc_final: 0.6520 (mmtm) REVERT: A 608 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 691 ASP cc_start: 0.6716 (m-30) cc_final: 0.6468 (m-30) REVERT: A 697 LYS cc_start: 0.7901 (tptt) cc_final: 0.7615 (tptt) REVERT: A 701 ASP cc_start: 0.7243 (t70) cc_final: 0.6773 (t0) REVERT: A 711 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7362 (mm-40) REVERT: A 769 MET cc_start: 0.8069 (mtp) cc_final: 0.7780 (mtm) REVERT: A 818 GLU cc_start: 0.7301 (tp30) cc_final: 0.6862 (tp30) REVERT: A 910 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8110 (mtmm) REVERT: A 940 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7625 (mtmm) REVERT: A 1023 VAL cc_start: 0.8295 (t) cc_final: 0.8021 (t) REVERT: A 1032 GLN cc_start: 0.7330 (tp40) cc_final: 0.7065 (tp40) REVERT: A 1078 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7567 (mm-40) REVERT: A 1132 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8084 (mtmm) REVERT: A 1211 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7107 (tt) REVERT: A 1218 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.8097 (tpp80) REVERT: A 1223 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: A 1306 LYS cc_start: 0.8057 (tptt) cc_final: 0.7325 (tptt) REVERT: A 1351 ASP cc_start: 0.7477 (t0) cc_final: 0.7062 (t0) REVERT: A 1361 ASP cc_start: 0.7150 (p0) cc_final: 0.6816 (p0) REVERT: A 1449 ASP cc_start: 0.7899 (t0) cc_final: 0.7561 (t0) REVERT: A 1455 SER cc_start: 0.8243 (p) cc_final: 0.7666 (m) REVERT: A 1472 ASP cc_start: 0.7623 (m-30) cc_final: 0.7392 (m-30) REVERT: A 1479 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7451 (mtpp) REVERT: B 92 TYR cc_start: 0.7494 (m-80) cc_final: 0.7200 (m-80) REVERT: B 106 SER cc_start: 0.7759 (t) cc_final: 0.7189 (m) REVERT: B 254 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6279 (mp-120) REVERT: B 286 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6012 (mt-10) REVERT: B 289 ILE cc_start: 0.8307 (mt) cc_final: 0.8024 (tt) REVERT: B 320 PHE cc_start: 0.7636 (t80) cc_final: 0.7399 (t80) REVERT: B 340 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7934 (mmmt) REVERT: B 345 LYS cc_start: 0.7699 (mmtp) cc_final: 0.7207 (mmtp) REVERT: B 363 TYR cc_start: 0.7839 (m-80) cc_final: 0.7545 (m-80) REVERT: B 413 LYS cc_start: 0.7769 (tttp) cc_final: 0.7429 (tttm) REVERT: B 432 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 433 LEU cc_start: 0.8364 (mt) cc_final: 0.7447 (mt) REVERT: B 438 ARG cc_start: 0.7061 (mmm160) cc_final: 0.6655 (mmm160) REVERT: B 497 LYS cc_start: 0.7741 (tptt) cc_final: 0.7444 (tptt) REVERT: B 510 CYS cc_start: 0.8271 (t) cc_final: 0.7629 (t) REVERT: B 581 GLU cc_start: 0.7333 (tt0) cc_final: 0.6995 (tt0) REVERT: B 629 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6624 (mm-30) REVERT: B 630 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7743 (mmtp) REVERT: B 637 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7907 (ttmm) REVERT: B 666 ASP cc_start: 0.7050 (p0) cc_final: 0.6690 (p0) REVERT: B 785 TYR cc_start: 0.7816 (t80) cc_final: 0.7268 (t80) REVERT: B 889 LYS cc_start: 0.7308 (mptt) cc_final: 0.6815 (mptt) REVERT: B 905 ASP cc_start: 0.6761 (t0) cc_final: 0.6517 (t0) REVERT: B 917 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8294 (ttmm) REVERT: B 1029 TYR cc_start: 0.8263 (m-80) cc_final: 0.8022 (m-10) REVERT: B 1052 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8439 (ptpt) REVERT: B 1060 HIS cc_start: 0.7721 (t70) cc_final: 0.7480 (t70) REVERT: B 1108 PHE cc_start: 0.8364 (t80) cc_final: 0.7962 (t80) REVERT: B 1148 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 30 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7707 (t) REVERT: C 41 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 59 LEU cc_start: 0.7829 (mt) cc_final: 0.7577 (mp) REVERT: C 97 CYS cc_start: 0.5306 (p) cc_final: 0.5006 (p) REVERT: C 104 ASP cc_start: 0.7596 (t0) cc_final: 0.7204 (t0) REVERT: C 121 ILE cc_start: 0.8358 (mm) cc_final: 0.8132 (mt) REVERT: C 152 LYS cc_start: 0.8654 (mttm) cc_final: 0.8394 (mttm) REVERT: C 185 GLU cc_start: 0.7207 (tt0) cc_final: 0.6988 (tt0) REVERT: C 229 PHE cc_start: 0.8525 (m-80) cc_final: 0.8193 (m-80) REVERT: C 253 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7365 (ttmm) REVERT: E 18 MET cc_start: 0.8327 (mmt) cc_final: 0.7953 (mmt) REVERT: E 35 GLN cc_start: 0.7899 (tt0) cc_final: 0.7575 (tt0) REVERT: E 61 LEU cc_start: 0.8875 (tp) cc_final: 0.8630 (tt) REVERT: E 64 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7689 (t-90) REVERT: E 73 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6521 (t80) REVERT: E 79 GLU cc_start: 0.7326 (mp0) cc_final: 0.6796 (mp0) REVERT: E 81 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7894 (mmpt) REVERT: E 86 THR cc_start: 0.8033 (t) cc_final: 0.7802 (t) REVERT: E 155 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6892 (mt-10) REVERT: E 166 ARG cc_start: 0.7602 (mtm180) cc_final: 0.6697 (mtm180) REVERT: E 197 SER cc_start: 0.8500 (p) cc_final: 0.7996 (m) REVERT: F 112 ASP cc_start: 0.8215 (p0) cc_final: 0.7972 (p0) REVERT: F 124 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7565 (mt) REVERT: G 131 MET cc_start: -0.0266 (mtp) cc_final: -0.0641 (mtp) REVERT: G 137 ILE cc_start: 0.2364 (OUTLIER) cc_final: 0.2101 (mp) REVERT: H 7 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6548 (tm-30) REVERT: H 42 ASP cc_start: 0.7636 (m-30) cc_final: 0.7226 (m-30) REVERT: H 52 LEU cc_start: 0.8636 (tp) cc_final: 0.8278 (tt) REVERT: H 64 LEU cc_start: 0.8153 (mt) cc_final: 0.7753 (mt) REVERT: H 122 LEU cc_start: 0.8223 (mt) cc_final: 0.7572 (mt) REVERT: H 124 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7627 (ttt-90) REVERT: I 46 GLN cc_start: 0.8030 (tt0) cc_final: 0.7458 (tm-30) REVERT: I 74 GLN cc_start: 0.7525 (pt0) cc_final: 0.7066 (pt0) REVERT: I 110 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8216 (mt) REVERT: J 53 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7802 (m) REVERT: J 62 TYR cc_start: 0.8170 (m-80) cc_final: 0.7898 (m-80) REVERT: K 23 LYS cc_start: 0.7760 (tptp) cc_final: 0.7246 (tptp) REVERT: K 50 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7980 (mt) REVERT: K 52 LYS cc_start: 0.8310 (mmtp) cc_final: 0.7886 (mmtp) REVERT: L 54 VAL cc_start: 0.8692 (t) cc_final: 0.8254 (m) REVERT: U 225 LEU cc_start: 0.7036 (mt) cc_final: 0.6809 (mt) REVERT: U 287 LYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3584 (tppp) REVERT: U 397 MET cc_start: 0.6735 (mtp) cc_final: 0.6194 (mtp) REVERT: U 510 LYS cc_start: 0.7595 (ptmm) cc_final: 0.7128 (ptmm) REVERT: U 541 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5598 (ptt180) REVERT: U 555 ARG cc_start: 0.6953 (mtm110) cc_final: 0.6354 (mtm110) REVERT: U 598 LYS cc_start: 0.7528 (mttt) cc_final: 0.7139 (mttt) outliers start: 211 outliers final: 164 residues processed: 1030 average time/residue: 0.2526 time to fit residues: 398.1084 Evaluate side-chains 1092 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 911 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Chi-restraints excluded: chain U residue 541 ARG Chi-restraints excluded: chain U residue 584 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 371 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 418 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN K 2 ASN K 76 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116178 restraints weight = 68703.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120098 restraints weight = 31599.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120727 restraints weight = 18486.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121837 restraints weight = 13938.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122278 restraints weight = 10766.056| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36662 Z= 0.176 Angle : 0.626 17.133 49742 Z= 0.314 Chirality : 0.045 0.218 5565 Planarity : 0.005 0.058 6258 Dihedral : 12.293 165.824 5499 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 5.31 % Allowed : 18.89 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.13), residues: 4314 helix: 0.97 (0.13), residues: 1589 sheet: -0.59 (0.21), residues: 577 loop : -1.12 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 172 TYR 0.020 0.001 TYR B 262 PHE 0.031 0.002 PHE A 234 TRP 0.017 0.001 TRP B 27 HIS 0.007 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00404 (36629) covalent geometry : angle 0.61595 (49695) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.24453 ( 2) hydrogen bonds : bond 0.03736 ( 1505) hydrogen bonds : angle 4.77632 ( 4231) metal coordination : bond 0.00943 ( 32) metal coordination : angle 3.80286 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 922 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8135 (t) cc_final: 0.7712 (p) REVERT: A 30 GLU cc_start: 0.7321 (tt0) cc_final: 0.7050 (tt0) REVERT: A 70 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7134 (mtp85) REVERT: A 104 MET cc_start: 0.7957 (mtp) cc_final: 0.7715 (mtp) REVERT: A 108 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7282 (mtm-85) REVERT: A 116 LYS cc_start: 0.7407 (mttm) cc_final: 0.7198 (mttm) REVERT: A 133 SER cc_start: 0.7939 (m) cc_final: 0.7597 (p) REVERT: A 238 MET cc_start: 0.8100 (mtp) cc_final: 0.7782 (mtt) REVERT: A 340 LYS cc_start: 0.8238 (tttt) cc_final: 0.8034 (ttmt) REVERT: A 347 GLU cc_start: 0.6810 (mp0) cc_final: 0.6324 (mp0) REVERT: A 417 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7945 (mtpt) REVERT: A 428 ASP cc_start: 0.7541 (t0) cc_final: 0.7169 (t70) REVERT: A 489 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7606 (p) REVERT: A 540 ASP cc_start: 0.7282 (m-30) cc_final: 0.7003 (m-30) REVERT: A 573 LYS cc_start: 0.6769 (mmtt) cc_final: 0.6562 (mmtm) REVERT: A 608 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7773 (t) REVERT: A 691 ASP cc_start: 0.6685 (m-30) cc_final: 0.6465 (m-30) REVERT: A 697 LYS cc_start: 0.7917 (tptt) cc_final: 0.7590 (tptt) REVERT: A 701 ASP cc_start: 0.7259 (t70) cc_final: 0.6764 (t0) REVERT: A 711 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 769 MET cc_start: 0.8109 (mtp) cc_final: 0.7804 (mtm) REVERT: A 818 GLU cc_start: 0.7248 (tp30) cc_final: 0.6981 (tp30) REVERT: A 910 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8110 (mtmm) REVERT: A 940 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7565 (mtmm) REVERT: A 1023 VAL cc_start: 0.8287 (t) cc_final: 0.8009 (t) REVERT: A 1032 GLN cc_start: 0.7315 (tp40) cc_final: 0.7108 (tp40) REVERT: A 1063 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: A 1078 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7548 (mm-40) REVERT: A 1132 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8066 (mtmm) REVERT: A 1189 ASP cc_start: 0.7248 (t70) cc_final: 0.6932 (t0) REVERT: A 1211 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7151 (tt) REVERT: A 1218 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8123 (tpp80) REVERT: A 1223 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: A 1306 LYS cc_start: 0.7973 (tptt) cc_final: 0.7244 (tptt) REVERT: A 1351 ASP cc_start: 0.7515 (t0) cc_final: 0.7112 (t0) REVERT: A 1361 ASP cc_start: 0.7151 (p0) cc_final: 0.6804 (p0) REVERT: A 1449 ASP cc_start: 0.7891 (t0) cc_final: 0.7619 (t0) REVERT: A 1455 SER cc_start: 0.8238 (p) cc_final: 0.7824 (t) REVERT: A 1479 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7442 (mtpp) REVERT: B 49 GLU cc_start: 0.6836 (tp30) cc_final: 0.6457 (tp30) REVERT: B 60 GLU cc_start: 0.7159 (tp30) cc_final: 0.6782 (tp30) REVERT: B 92 TYR cc_start: 0.7450 (m-80) cc_final: 0.7185 (m-80) REVERT: B 106 SER cc_start: 0.7757 (t) cc_final: 0.7161 (m) REVERT: B 148 PHE cc_start: 0.8286 (t80) cc_final: 0.8010 (t80) REVERT: B 274 ARG cc_start: 0.8482 (ttm110) cc_final: 0.8135 (mtm-85) REVERT: B 286 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5980 (mt-10) REVERT: B 296 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6976 (mm-30) REVERT: B 320 PHE cc_start: 0.7596 (t80) cc_final: 0.7211 (t80) REVERT: B 340 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7936 (mmmt) REVERT: B 345 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7203 (mmtp) REVERT: B 363 TYR cc_start: 0.7845 (m-80) cc_final: 0.7532 (m-80) REVERT: B 388 TYR cc_start: 0.7960 (t80) cc_final: 0.7136 (t80) REVERT: B 413 LYS cc_start: 0.7739 (tttp) cc_final: 0.7426 (tttm) REVERT: B 432 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 433 LEU cc_start: 0.8388 (mt) cc_final: 0.7657 (mt) REVERT: B 497 LYS cc_start: 0.7781 (tptt) cc_final: 0.7505 (tptt) REVERT: B 510 CYS cc_start: 0.8276 (t) cc_final: 0.7603 (t) REVERT: B 581 GLU cc_start: 0.7295 (tt0) cc_final: 0.6938 (tt0) REVERT: B 629 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6613 (mm-30) REVERT: B 630 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7752 (mmtp) REVERT: B 637 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7887 (ttmm) REVERT: B 666 ASP cc_start: 0.7021 (p0) cc_final: 0.6683 (p0) REVERT: B 785 TYR cc_start: 0.7773 (t80) cc_final: 0.7240 (t80) REVERT: B 817 GLN cc_start: 0.7728 (tt0) cc_final: 0.7480 (tt0) REVERT: B 889 LYS cc_start: 0.7296 (mptt) cc_final: 0.6796 (mptt) REVERT: B 905 ASP cc_start: 0.6743 (t0) cc_final: 0.6451 (t0) REVERT: B 917 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8169 (tttm) REVERT: B 983 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 1029 TYR cc_start: 0.8249 (m-80) cc_final: 0.8009 (m-10) REVERT: B 1052 LYS cc_start: 0.8668 (ptmm) cc_final: 0.8446 (ptpt) REVERT: B 1060 HIS cc_start: 0.7705 (t70) cc_final: 0.7463 (t70) REVERT: B 1108 PHE cc_start: 0.8406 (t80) cc_final: 0.7941 (t80) REVERT: B 1112 ASP cc_start: 0.7220 (p0) cc_final: 0.6999 (p0) REVERT: C 30 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7778 (t) REVERT: C 41 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7050 (mm-30) REVERT: C 59 LEU cc_start: 0.7874 (mt) cc_final: 0.7662 (mp) REVERT: C 86 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6392 (ptm160) REVERT: C 97 CYS cc_start: 0.5340 (p) cc_final: 0.5007 (p) REVERT: C 104 ASP cc_start: 0.7569 (t0) cc_final: 0.7218 (t0) REVERT: C 121 ILE cc_start: 0.8328 (mm) cc_final: 0.8097 (mt) REVERT: C 152 LYS cc_start: 0.8631 (mttm) cc_final: 0.8318 (mttm) REVERT: C 229 PHE cc_start: 0.8501 (m-80) cc_final: 0.8259 (m-80) REVERT: C 253 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7384 (ttmm) REVERT: E 35 GLN cc_start: 0.7877 (tt0) cc_final: 0.7654 (tt0) REVERT: E 64 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7675 (t-90) REVERT: E 73 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6545 (t80) REVERT: E 79 GLU cc_start: 0.7325 (mp0) cc_final: 0.6804 (mp0) REVERT: E 81 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7875 (mmpt) REVERT: E 86 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7765 (t) REVERT: E 155 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6883 (mt-10) REVERT: E 166 ARG cc_start: 0.7561 (mtm180) cc_final: 0.6683 (mtm180) REVERT: E 197 SER cc_start: 0.8506 (p) cc_final: 0.7981 (m) REVERT: F 124 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7577 (mt) REVERT: G 131 MET cc_start: -0.0295 (mtp) cc_final: -0.0669 (mtp) REVERT: G 137 ILE cc_start: 0.2228 (OUTLIER) cc_final: 0.1923 (mp) REVERT: H 7 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6488 (tm-30) REVERT: H 42 ASP cc_start: 0.7624 (m-30) cc_final: 0.7209 (m-30) REVERT: H 52 LEU cc_start: 0.8604 (tp) cc_final: 0.8266 (tt) REVERT: H 64 LEU cc_start: 0.8139 (mt) cc_final: 0.7740 (mt) REVERT: H 122 LEU cc_start: 0.8206 (mt) cc_final: 0.7562 (mt) REVERT: H 124 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7689 (ttt-90) REVERT: I 46 GLN cc_start: 0.7975 (tt0) cc_final: 0.7453 (tm-30) REVERT: I 74 GLN cc_start: 0.7527 (pt0) cc_final: 0.7127 (pt0) REVERT: I 110 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8206 (mt) REVERT: J 53 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7823 (m) REVERT: J 62 TYR cc_start: 0.8146 (m-80) cc_final: 0.7821 (m-80) REVERT: K 23 LYS cc_start: 0.7741 (tptp) cc_final: 0.7229 (tptp) REVERT: K 50 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7981 (mt) REVERT: K 52 LYS cc_start: 0.8324 (mmtp) cc_final: 0.7881 (mmtp) REVERT: L 54 VAL cc_start: 0.8683 (t) cc_final: 0.8223 (m) REVERT: U 225 LEU cc_start: 0.7042 (mt) cc_final: 0.6811 (mt) REVERT: U 287 LYS cc_start: 0.4312 (OUTLIER) cc_final: 0.3844 (tppp) REVERT: U 397 MET cc_start: 0.6692 (mtp) cc_final: 0.6154 (mtp) REVERT: U 510 LYS cc_start: 0.7592 (ptmm) cc_final: 0.7126 (ptmm) REVERT: U 555 ARG cc_start: 0.6953 (mtm110) cc_final: 0.6355 (mtm110) REVERT: U 598 LYS cc_start: 0.7533 (mttt) cc_final: 0.7140 (mttt) outliers start: 203 outliers final: 165 residues processed: 1036 average time/residue: 0.2626 time to fit residues: 414.9399 Evaluate side-chains 1091 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 909 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 416 ILE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 415 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 337 optimal weight: 0.2980 chunk 364 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 234 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 331 optimal weight: 3.9990 chunk 381 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 76 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117161 restraints weight = 81894.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121161 restraints weight = 35861.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122446 restraints weight = 18408.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123158 restraints weight = 13900.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123355 restraints weight = 11043.814| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36662 Z= 0.143 Angle : 0.613 16.150 49742 Z= 0.308 Chirality : 0.044 0.191 5565 Planarity : 0.004 0.058 6258 Dihedral : 12.185 167.616 5497 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.05 % Favored : 93.74 % Rotamer: Outliers : 4.87 % Allowed : 19.70 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.13), residues: 4314 helix: 1.05 (0.13), residues: 1593 sheet: -0.59 (0.21), residues: 586 loop : -1.09 (0.14), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 172 TYR 0.019 0.001 TYR B 262 PHE 0.027 0.001 PHE B 148 TRP 0.016 0.001 TRP B 27 HIS 0.015 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00328 (36629) covalent geometry : angle 0.60490 (49695) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.28135 ( 2) hydrogen bonds : bond 0.03496 ( 1505) hydrogen bonds : angle 4.69640 ( 4231) metal coordination : bond 0.00690 ( 32) metal coordination : angle 3.38634 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 924 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8153 (t) cc_final: 0.7695 (p) REVERT: A 70 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7128 (mtp85) REVERT: A 104 MET cc_start: 0.7986 (mtp) cc_final: 0.7738 (mtp) REVERT: A 108 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7297 (mtm-85) REVERT: A 116 LYS cc_start: 0.7394 (mttm) cc_final: 0.7146 (mttm) REVERT: A 133 SER cc_start: 0.7949 (m) cc_final: 0.7606 (p) REVERT: A 148 CYS cc_start: 0.7949 (p) cc_final: 0.7712 (p) REVERT: A 234 PHE cc_start: 0.7834 (t80) cc_final: 0.7603 (t80) REVERT: A 238 MET cc_start: 0.8092 (mtp) cc_final: 0.7771 (mtt) REVERT: A 340 LYS cc_start: 0.8223 (tttt) cc_final: 0.7846 (ttmt) REVERT: A 347 GLU cc_start: 0.6737 (mp0) cc_final: 0.6261 (mp0) REVERT: A 358 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7854 (mtt90) REVERT: A 417 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7951 (mtpt) REVERT: A 428 ASP cc_start: 0.7434 (t0) cc_final: 0.7097 (t70) REVERT: A 489 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7593 (p) REVERT: A 540 ASP cc_start: 0.7255 (m-30) cc_final: 0.6874 (m-30) REVERT: A 608 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7745 (t) REVERT: A 627 LYS cc_start: 0.8549 (tppt) cc_final: 0.8290 (tppt) REVERT: A 697 LYS cc_start: 0.7906 (tptt) cc_final: 0.7544 (tptt) REVERT: A 701 ASP cc_start: 0.7268 (t70) cc_final: 0.6810 (t0) REVERT: A 711 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7278 (mm-40) REVERT: A 769 MET cc_start: 0.8072 (mtp) cc_final: 0.7788 (mtm) REVERT: A 910 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8102 (mtmm) REVERT: A 916 PHE cc_start: 0.7855 (t80) cc_final: 0.7617 (t80) REVERT: A 940 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7491 (mtmm) REVERT: A 976 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: A 1023 VAL cc_start: 0.8279 (t) cc_final: 0.7976 (t) REVERT: A 1032 GLN cc_start: 0.7254 (tp40) cc_final: 0.7053 (tp40) REVERT: A 1050 CYS cc_start: 0.7334 (t) cc_final: 0.6856 (t) REVERT: A 1063 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6452 (tt0) REVERT: A 1132 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8081 (mtmm) REVERT: A 1189 ASP cc_start: 0.7399 (t70) cc_final: 0.7084 (t0) REVERT: A 1211 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7060 (tt) REVERT: A 1218 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8084 (tpp80) REVERT: A 1223 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6523 (m-30) REVERT: A 1306 LYS cc_start: 0.7960 (tptt) cc_final: 0.7185 (tptt) REVERT: A 1351 ASP cc_start: 0.7520 (t0) cc_final: 0.7141 (t0) REVERT: A 1361 ASP cc_start: 0.7152 (p0) cc_final: 0.6803 (p0) REVERT: A 1449 ASP cc_start: 0.7900 (t0) cc_final: 0.7418 (t0) REVERT: A 1455 SER cc_start: 0.8203 (p) cc_final: 0.7903 (t) REVERT: A 1479 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7481 (mtpp) REVERT: B 49 GLU cc_start: 0.6807 (tp30) cc_final: 0.6419 (tp30) REVERT: B 60 GLU cc_start: 0.7083 (tp30) cc_final: 0.6758 (tp30) REVERT: B 92 TYR cc_start: 0.7390 (m-80) cc_final: 0.7128 (m-80) REVERT: B 106 SER cc_start: 0.7770 (t) cc_final: 0.7128 (m) REVERT: B 148 PHE cc_start: 0.8280 (t80) cc_final: 0.7993 (t80) REVERT: B 274 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8134 (mtm-85) REVERT: B 286 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6022 (mt-10) REVERT: B 320 PHE cc_start: 0.7499 (t80) cc_final: 0.7141 (t80) REVERT: B 340 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7943 (mmmt) REVERT: B 345 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7238 (mmtp) REVERT: B 363 TYR cc_start: 0.7900 (m-80) cc_final: 0.7577 (m-80) REVERT: B 380 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7397 (mmt90) REVERT: B 413 LYS cc_start: 0.7658 (tttp) cc_final: 0.7349 (tttm) REVERT: B 432 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 433 LEU cc_start: 0.8346 (mt) cc_final: 0.7354 (mt) REVERT: B 497 LYS cc_start: 0.7781 (tptt) cc_final: 0.7486 (tptt) REVERT: B 510 CYS cc_start: 0.8248 (t) cc_final: 0.7581 (t) REVERT: B 581 GLU cc_start: 0.7272 (tt0) cc_final: 0.6920 (tt0) REVERT: B 629 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6614 (mm-30) REVERT: B 630 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7756 (mmtp) REVERT: B 637 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7887 (ttmm) REVERT: B 666 ASP cc_start: 0.7029 (p0) cc_final: 0.6665 (p0) REVERT: B 785 TYR cc_start: 0.7735 (t80) cc_final: 0.7217 (t80) REVERT: B 817 GLN cc_start: 0.7685 (tt0) cc_final: 0.7469 (tt0) REVERT: B 889 LYS cc_start: 0.7207 (mptt) cc_final: 0.6654 (mptt) REVERT: B 905 ASP cc_start: 0.6738 (t0) cc_final: 0.6464 (t0) REVERT: B 917 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8137 (tttm) REVERT: B 1029 TYR cc_start: 0.8236 (m-80) cc_final: 0.7958 (m-10) REVERT: B 1052 LYS cc_start: 0.8644 (ptmm) cc_final: 0.8432 (ptpt) REVERT: B 1060 HIS cc_start: 0.7695 (t70) cc_final: 0.7425 (t70) REVERT: B 1108 PHE cc_start: 0.8355 (t80) cc_final: 0.7901 (t80) REVERT: B 1112 ASP cc_start: 0.7223 (p0) cc_final: 0.7005 (p0) REVERT: C 30 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7691 (t) REVERT: C 41 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 86 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6373 (ptm160) REVERT: C 97 CYS cc_start: 0.5398 (p) cc_final: 0.5058 (p) REVERT: C 104 ASP cc_start: 0.7562 (t0) cc_final: 0.7224 (t0) REVERT: C 121 ILE cc_start: 0.8316 (mm) cc_final: 0.8088 (mt) REVERT: C 152 LYS cc_start: 0.8565 (mttm) cc_final: 0.8282 (mttm) REVERT: C 210 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6538 (mm-30) REVERT: C 253 LYS cc_start: 0.7567 (ttmm) cc_final: 0.7324 (ttmm) REVERT: E 35 GLN cc_start: 0.7845 (tt0) cc_final: 0.7643 (tt0) REVERT: E 64 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: E 73 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6474 (t80) REVERT: E 79 GLU cc_start: 0.7348 (mp0) cc_final: 0.6814 (mp0) REVERT: E 81 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7869 (mmpt) REVERT: E 86 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7750 (t) REVERT: E 155 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6896 (mt-10) REVERT: E 166 ARG cc_start: 0.7590 (mtm180) cc_final: 0.6791 (mtm180) REVERT: E 197 SER cc_start: 0.8457 (p) cc_final: 0.7941 (m) REVERT: F 124 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7584 (mt) REVERT: G 131 MET cc_start: -0.0246 (mtp) cc_final: -0.0632 (mtp) REVERT: G 137 ILE cc_start: 0.2199 (OUTLIER) cc_final: 0.1911 (mp) REVERT: H 7 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6471 (tm-30) REVERT: H 42 ASP cc_start: 0.7562 (m-30) cc_final: 0.7144 (m-30) REVERT: H 52 LEU cc_start: 0.8569 (tp) cc_final: 0.8308 (tt) REVERT: H 64 LEU cc_start: 0.8109 (mt) cc_final: 0.7728 (mt) REVERT: H 122 LEU cc_start: 0.8262 (mt) cc_final: 0.7571 (mt) REVERT: H 124 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7620 (ttt-90) REVERT: I 36 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7138 (mm) REVERT: I 46 GLN cc_start: 0.7977 (tt0) cc_final: 0.7406 (tm-30) REVERT: I 74 GLN cc_start: 0.7508 (pt0) cc_final: 0.7126 (pt0) REVERT: I 110 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (mt) REVERT: J 53 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7762 (m) REVERT: J 62 TYR cc_start: 0.8128 (m-80) cc_final: 0.7784 (m-80) REVERT: K 23 LYS cc_start: 0.7698 (tptp) cc_final: 0.7161 (tptp) REVERT: K 50 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7983 (mt) REVERT: K 52 LYS cc_start: 0.8338 (mmtp) cc_final: 0.7895 (mmtp) REVERT: L 54 VAL cc_start: 0.8628 (t) cc_final: 0.8101 (m) REVERT: U 225 LEU cc_start: 0.7044 (mt) cc_final: 0.6808 (mt) REVERT: U 282 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6614 (mtm-85) REVERT: U 287 LYS cc_start: 0.4445 (OUTLIER) cc_final: 0.4044 (tppp) REVERT: U 397 MET cc_start: 0.6673 (mtp) cc_final: 0.6146 (mtp) REVERT: U 510 LYS cc_start: 0.7575 (ptmm) cc_final: 0.7132 (ptmm) REVERT: U 555 ARG cc_start: 0.6961 (mtm110) cc_final: 0.6353 (mtm110) REVERT: U 598 LYS cc_start: 0.7529 (mttt) cc_final: 0.7136 (mttt) outliers start: 186 outliers final: 139 residues processed: 1030 average time/residue: 0.2534 time to fit residues: 399.3131 Evaluate side-chains 1067 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 908 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain A residue 1416 ARG Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 275 LEU Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 416 ILE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 253 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 395 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 375 optimal weight: 0.9990 chunk 256 optimal weight: 0.0370 chunk 337 optimal weight: 0.0770 chunk 117 optimal weight: 0.7980 chunk 389 optimal weight: 0.3980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 141 GLN B 145 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN K 2 ASN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119736 restraints weight = 62505.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122908 restraints weight = 28907.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123561 restraints weight = 18692.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124527 restraints weight = 13926.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126164 restraints weight = 11135.432| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 36662 Z= 0.123 Angle : 0.610 15.811 49742 Z= 0.305 Chirality : 0.044 0.194 5565 Planarity : 0.004 0.058 6258 Dihedral : 12.036 169.583 5486 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.73 % Favored : 94.06 % Rotamer: Outliers : 4.37 % Allowed : 20.57 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4314 helix: 1.11 (0.13), residues: 1594 sheet: -0.57 (0.21), residues: 595 loop : -1.06 (0.14), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 240 TYR 0.020 0.001 TYR B 262 PHE 0.027 0.001 PHE B 148 TRP 0.014 0.001 TRP B 27 HIS 0.011 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00284 (36629) covalent geometry : angle 0.60374 (49695) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.30766 ( 2) hydrogen bonds : bond 0.03310 ( 1505) hydrogen bonds : angle 4.60261 ( 4231) metal coordination : bond 0.00505 ( 32) metal coordination : angle 3.07357 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 944 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8045 (t) cc_final: 0.7708 (p) REVERT: A 30 GLU cc_start: 0.7151 (tt0) cc_final: 0.6378 (tt0) REVERT: A 33 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7012 (mtm110) REVERT: A 70 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7124 (mtp85) REVERT: A 104 MET cc_start: 0.7983 (mtp) cc_final: 0.7755 (mtp) REVERT: A 108 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7230 (mtm-85) REVERT: A 116 LYS cc_start: 0.7349 (mttm) cc_final: 0.7147 (mttm) REVERT: A 133 SER cc_start: 0.7932 (m) cc_final: 0.7634 (p) REVERT: A 234 PHE cc_start: 0.7836 (t80) cc_final: 0.7610 (t80) REVERT: A 238 MET cc_start: 0.8116 (mtp) cc_final: 0.7798 (mtt) REVERT: A 340 LYS cc_start: 0.8179 (tttt) cc_final: 0.7759 (tttp) REVERT: A 347 GLU cc_start: 0.6722 (mp0) cc_final: 0.6204 (mp0) REVERT: A 417 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7947 (mtpt) REVERT: A 428 ASP cc_start: 0.7451 (t0) cc_final: 0.7091 (t70) REVERT: A 489 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 540 ASP cc_start: 0.7131 (m-30) cc_final: 0.6766 (m-30) REVERT: A 565 MET cc_start: 0.7758 (mmm) cc_final: 0.7459 (ttm) REVERT: A 608 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7689 (t) REVERT: A 627 LYS cc_start: 0.8559 (tppt) cc_final: 0.8334 (tppt) REVERT: A 648 SER cc_start: 0.7801 (p) cc_final: 0.7577 (m) REVERT: A 697 LYS cc_start: 0.7805 (tptt) cc_final: 0.7510 (tptt) REVERT: A 701 ASP cc_start: 0.7223 (t70) cc_final: 0.6777 (t0) REVERT: A 711 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7298 (mm-40) REVERT: A 738 GLU cc_start: 0.7417 (tp30) cc_final: 0.7212 (tp30) REVERT: A 769 MET cc_start: 0.7979 (mtp) cc_final: 0.7742 (mtm) REVERT: A 910 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8122 (mtmm) REVERT: A 916 PHE cc_start: 0.7859 (t80) cc_final: 0.7610 (t80) REVERT: A 922 PHE cc_start: 0.8604 (t80) cc_final: 0.8343 (t80) REVERT: A 940 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7486 (mtmm) REVERT: A 976 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: A 1023 VAL cc_start: 0.8218 (t) cc_final: 0.7965 (t) REVERT: A 1054 MET cc_start: 0.8173 (tpp) cc_final: 0.7738 (mmm) REVERT: A 1063 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: A 1132 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8048 (mtmm) REVERT: A 1189 ASP cc_start: 0.7230 (t70) cc_final: 0.6952 (t0) REVERT: A 1211 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 1218 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8048 (tpp80) REVERT: A 1223 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: A 1306 LYS cc_start: 0.7913 (tptt) cc_final: 0.7125 (tptt) REVERT: A 1351 ASP cc_start: 0.7536 (t0) cc_final: 0.7208 (t0) REVERT: A 1361 ASP cc_start: 0.7111 (p0) cc_final: 0.6768 (p0) REVERT: A 1363 VAL cc_start: 0.7401 (t) cc_final: 0.7069 (m) REVERT: A 1440 MET cc_start: 0.7998 (mmt) cc_final: 0.7558 (mmt) REVERT: A 1449 ASP cc_start: 0.7870 (t0) cc_final: 0.7524 (t0) REVERT: A 1451 MET cc_start: 0.7545 (mmm) cc_final: 0.7296 (mmm) REVERT: A 1455 SER cc_start: 0.8176 (p) cc_final: 0.7780 (t) REVERT: A 1459 MET cc_start: 0.7197 (mtp) cc_final: 0.6969 (mtm) REVERT: A 1472 ASP cc_start: 0.7657 (m-30) cc_final: 0.7376 (m-30) REVERT: A 1479 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7481 (mtpp) REVERT: B 41 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7702 (tpp80) REVERT: B 49 GLU cc_start: 0.6817 (tp30) cc_final: 0.6395 (tp30) REVERT: B 60 GLU cc_start: 0.7035 (tp30) cc_final: 0.6675 (mm-30) REVERT: B 92 TYR cc_start: 0.7339 (m-80) cc_final: 0.7107 (m-80) REVERT: B 106 SER cc_start: 0.7719 (t) cc_final: 0.7098 (m) REVERT: B 148 PHE cc_start: 0.8256 (t80) cc_final: 0.7992 (t80) REVERT: B 255 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7738 (mtp-110) REVERT: B 274 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8144 (mtm-85) REVERT: B 286 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5947 (mt-10) REVERT: B 320 PHE cc_start: 0.7397 (t80) cc_final: 0.7167 (t80) REVERT: B 340 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7934 (mmmt) REVERT: B 345 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7202 (mmtp) REVERT: B 361 LYS cc_start: 0.7668 (mttp) cc_final: 0.7221 (mttt) REVERT: B 363 TYR cc_start: 0.7871 (m-80) cc_final: 0.7542 (m-80) REVERT: B 388 TYR cc_start: 0.7887 (t80) cc_final: 0.7098 (t80) REVERT: B 394 ASP cc_start: 0.7054 (m-30) cc_final: 0.6742 (p0) REVERT: B 432 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7060 (tm-30) REVERT: B 433 LEU cc_start: 0.8367 (mt) cc_final: 0.7548 (mt) REVERT: B 497 LYS cc_start: 0.7741 (tptt) cc_final: 0.7447 (tptt) REVERT: B 510 CYS cc_start: 0.8276 (t) cc_final: 0.7616 (t) REVERT: B 581 GLU cc_start: 0.7232 (tt0) cc_final: 0.6913 (tt0) REVERT: B 629 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6610 (mm-30) REVERT: B 630 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7711 (mmtp) REVERT: B 637 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7900 (ttmm) REVERT: B 666 ASP cc_start: 0.7045 (p0) cc_final: 0.6672 (p0) REVERT: B 849 ASP cc_start: 0.7592 (t0) cc_final: 0.7318 (m-30) REVERT: B 889 LYS cc_start: 0.7292 (mptt) cc_final: 0.6804 (mptt) REVERT: B 905 ASP cc_start: 0.6725 (t0) cc_final: 0.6447 (t0) REVERT: B 917 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8111 (tttm) REVERT: B 959 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 976 MET cc_start: 0.7447 (mtm) cc_final: 0.7233 (mtt) REVERT: B 1060 HIS cc_start: 0.7664 (t70) cc_final: 0.7393 (t70) REVERT: B 1108 PHE cc_start: 0.8359 (t80) cc_final: 0.7989 (t80) REVERT: B 1112 ASP cc_start: 0.7209 (p0) cc_final: 0.6965 (p0) REVERT: B 1148 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8170 (tt) REVERT: C 30 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7708 (t) REVERT: C 41 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7026 (mm-30) REVERT: C 97 CYS cc_start: 0.5331 (p) cc_final: 0.4956 (p) REVERT: C 104 ASP cc_start: 0.7554 (t0) cc_final: 0.7228 (t0) REVERT: C 121 ILE cc_start: 0.8292 (mm) cc_final: 0.8067 (mt) REVERT: C 152 LYS cc_start: 0.8561 (mttm) cc_final: 0.8331 (mttm) REVERT: C 210 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6470 (mm-30) REVERT: C 253 LYS cc_start: 0.7518 (ttmm) cc_final: 0.7254 (ttmm) REVERT: E 35 GLN cc_start: 0.7880 (tt0) cc_final: 0.7649 (tt0) REVERT: E 64 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: E 73 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6530 (t80) REVERT: E 79 GLU cc_start: 0.7318 (mp0) cc_final: 0.6814 (mp0) REVERT: E 81 LYS cc_start: 0.8093 (mmpt) cc_final: 0.7839 (mmpt) REVERT: E 86 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7756 (t) REVERT: E 150 VAL cc_start: 0.8556 (t) cc_final: 0.8211 (m) REVERT: E 155 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6937 (mt-10) REVERT: E 166 ARG cc_start: 0.7524 (mtm180) cc_final: 0.6812 (mtm180) REVERT: E 197 SER cc_start: 0.8498 (p) cc_final: 0.8040 (m) REVERT: F 101 LYS cc_start: 0.8000 (mmtp) cc_final: 0.7795 (mmtp) REVERT: F 124 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7673 (mt) REVERT: G 131 MET cc_start: -0.0393 (mtp) cc_final: -0.0775 (mtp) REVERT: G 137 ILE cc_start: 0.2193 (OUTLIER) cc_final: 0.1893 (mp) REVERT: H 7 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6397 (tm-30) REVERT: H 42 ASP cc_start: 0.7607 (m-30) cc_final: 0.7146 (m-30) REVERT: H 52 LEU cc_start: 0.8523 (tp) cc_final: 0.8246 (tt) REVERT: H 64 LEU cc_start: 0.8135 (mt) cc_final: 0.7747 (mt) REVERT: H 122 LEU cc_start: 0.8215 (mt) cc_final: 0.7565 (mt) REVERT: H 124 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7661 (ttt-90) REVERT: I 46 GLN cc_start: 0.7960 (tt0) cc_final: 0.7443 (tm-30) REVERT: I 55 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7134 (t) REVERT: J 53 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7782 (m) REVERT: J 62 TYR cc_start: 0.8140 (m-80) cc_final: 0.7809 (m-80) REVERT: K 23 LYS cc_start: 0.7659 (tptp) cc_final: 0.7133 (tptp) REVERT: K 50 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7584 (mp) REVERT: K 52 LYS cc_start: 0.8345 (mmtp) cc_final: 0.7934 (mmtp) REVERT: L 54 VAL cc_start: 0.8548 (t) cc_final: 0.8074 (m) REVERT: U 225 LEU cc_start: 0.7002 (mt) cc_final: 0.6702 (mt) REVERT: U 282 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6546 (mtm-85) REVERT: U 397 MET cc_start: 0.6611 (mtp) cc_final: 0.6091 (mtp) REVERT: U 510 LYS cc_start: 0.7520 (ptmm) cc_final: 0.7110 (ptmm) REVERT: U 555 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6350 (mtm110) REVERT: U 598 LYS cc_start: 0.7526 (mttt) cc_final: 0.7131 (mttt) outliers start: 167 outliers final: 131 residues processed: 1039 average time/residue: 0.2638 time to fit residues: 419.2821 Evaluate side-chains 1058 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 909 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 416 ILE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 70 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 217 optimal weight: 3.9990 chunk 416 optimal weight: 20.0000 chunk 409 optimal weight: 8.9990 chunk 272 optimal weight: 0.5980 chunk 401 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 55 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118437 restraints weight = 60030.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122225 restraints weight = 27335.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122675 restraints weight = 15795.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123627 restraints weight = 13124.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125294 restraints weight = 10302.270| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36662 Z= 0.156 Angle : 0.632 16.413 49742 Z= 0.315 Chirality : 0.045 0.198 5565 Planarity : 0.005 0.060 6258 Dihedral : 11.961 170.306 5475 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.92 % Favored : 93.88 % Rotamer: Outliers : 4.13 % Allowed : 20.96 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4314 helix: 1.10 (0.13), residues: 1593 sheet: -0.59 (0.21), residues: 603 loop : -1.06 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 37 TYR 0.022 0.001 TYR B 262 PHE 0.023 0.001 PHE B 148 TRP 0.016 0.001 TRP B 27 HIS 0.011 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00364 (36629) covalent geometry : angle 0.62407 (49695) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.24616 ( 2) hydrogen bonds : bond 0.03474 ( 1505) hydrogen bonds : angle 4.59611 ( 4231) metal coordination : bond 0.00773 ( 32) metal coordination : angle 3.30144 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 914 time to evaluate : 1.096 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 27 SER cc_start: 0.8043 (t) cc_final: 0.7702 (p) REVERT: A 70 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7166 (mtp85) REVERT: A 108 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7186 (mtm-85) REVERT: A 116 LYS cc_start: 0.7388 (mttm) cc_final: 0.7175 (mttm) REVERT: A 133 SER cc_start: 0.7936 (m) cc_final: 0.7610 (p) REVERT: A 234 PHE cc_start: 0.7834 (t80) cc_final: 0.7607 (t80) REVERT: A 238 MET cc_start: 0.8123 (mtp) cc_final: 0.7694 (mtm) REVERT: A 340 LYS cc_start: 0.8224 (tttt) cc_final: 0.7784 (tttp) REVERT: A 347 GLU cc_start: 0.6779 (mp0) cc_final: 0.6223 (mp0) REVERT: A 355 MET cc_start: 0.8282 (mmp) cc_final: 0.8062 (mmp) REVERT: A 417 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7941 (mtpt) REVERT: A 428 ASP cc_start: 0.7468 (t0) cc_final: 0.7122 (t70) REVERT: A 489 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 540 ASP cc_start: 0.7154 (m-30) cc_final: 0.6771 (m-30) REVERT: A 608 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 627 LYS cc_start: 0.8425 (tppt) cc_final: 0.7910 (mmtt) REVERT: A 648 SER cc_start: 0.7836 (p) cc_final: 0.7596 (m) REVERT: A 697 LYS cc_start: 0.7846 (tptt) cc_final: 0.7551 (tptt) REVERT: A 701 ASP cc_start: 0.7260 (t70) cc_final: 0.6845 (t0) REVERT: A 711 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 738 GLU cc_start: 0.7428 (tp30) cc_final: 0.7214 (tp30) REVERT: A 868 MET cc_start: 0.6847 (mtp) cc_final: 0.6615 (mtm) REVERT: A 910 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8078 (mtmm) REVERT: A 916 PHE cc_start: 0.7924 (t80) cc_final: 0.7685 (t80) REVERT: A 940 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7466 (mtmm) REVERT: A 976 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8248 (ttpp) REVERT: A 1063 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: A 1132 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8100 (mtmm) REVERT: A 1139 LEU cc_start: 0.7983 (tp) cc_final: 0.7736 (tt) REVERT: A 1167 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.7200 (ttm-80) REVERT: A 1189 ASP cc_start: 0.7225 (t70) cc_final: 0.6872 (t0) REVERT: A 1211 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7120 (tt) REVERT: A 1215 GLU cc_start: 0.6602 (mp0) cc_final: 0.6050 (mp0) REVERT: A 1223 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: A 1306 LYS cc_start: 0.7916 (tptt) cc_final: 0.7163 (tptt) REVERT: A 1351 ASP cc_start: 0.7545 (t0) cc_final: 0.7206 (t0) REVERT: A 1361 ASP cc_start: 0.7103 (p0) cc_final: 0.6779 (p0) REVERT: A 1372 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 1449 ASP cc_start: 0.7935 (t0) cc_final: 0.7491 (t0) REVERT: A 1451 MET cc_start: 0.7587 (mmm) cc_final: 0.7281 (mmm) REVERT: A 1455 SER cc_start: 0.8215 (p) cc_final: 0.7784 (t) REVERT: A 1459 MET cc_start: 0.7277 (mtp) cc_final: 0.6998 (mtm) REVERT: A 1472 ASP cc_start: 0.7639 (m-30) cc_final: 0.7410 (m-30) REVERT: A 1479 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7498 (mtpp) REVERT: B 49 GLU cc_start: 0.6818 (tp30) cc_final: 0.6414 (tp30) REVERT: B 60 GLU cc_start: 0.7060 (tp30) cc_final: 0.6711 (mm-30) REVERT: B 92 TYR cc_start: 0.7370 (m-80) cc_final: 0.7141 (m-80) REVERT: B 106 SER cc_start: 0.7731 (t) cc_final: 0.7095 (m) REVERT: B 148 PHE cc_start: 0.8274 (t80) cc_final: 0.8020 (t80) REVERT: B 254 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6211 (mp-120) REVERT: B 274 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8147 (mtm-85) REVERT: B 286 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5991 (mt-10) REVERT: B 320 PHE cc_start: 0.7448 (t80) cc_final: 0.7211 (t80) REVERT: B 340 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7947 (mmmt) REVERT: B 345 LYS cc_start: 0.7598 (mmtp) cc_final: 0.7185 (mmtp) REVERT: B 363 TYR cc_start: 0.7864 (m-80) cc_final: 0.7511 (m-80) REVERT: B 394 ASP cc_start: 0.7067 (m-30) cc_final: 0.6773 (p0) REVERT: B 432 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7100 (tm-30) REVERT: B 433 LEU cc_start: 0.8383 (mt) cc_final: 0.7663 (mt) REVERT: B 497 LYS cc_start: 0.7771 (tptt) cc_final: 0.7471 (tptt) REVERT: B 510 CYS cc_start: 0.8229 (t) cc_final: 0.7627 (t) REVERT: B 629 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6629 (mm-30) REVERT: B 630 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7705 (mmtp) REVERT: B 666 ASP cc_start: 0.7041 (p0) cc_final: 0.6665 (p0) REVERT: B 667 THR cc_start: 0.7876 (m) cc_final: 0.7640 (m) REVERT: B 785 TYR cc_start: 0.7710 (t80) cc_final: 0.7128 (t80) REVERT: B 849 ASP cc_start: 0.7602 (t0) cc_final: 0.7330 (m-30) REVERT: B 889 LYS cc_start: 0.7332 (mptt) cc_final: 0.7118 (mptt) REVERT: B 905 ASP cc_start: 0.6724 (t0) cc_final: 0.6477 (t0) REVERT: B 917 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8107 (tttm) REVERT: B 959 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 1060 HIS cc_start: 0.7703 (t70) cc_final: 0.7436 (t70) REVERT: B 1108 PHE cc_start: 0.8388 (t80) cc_final: 0.7950 (t80) REVERT: B 1134 THR cc_start: 0.8323 (t) cc_final: 0.8075 (m) REVERT: C 15 THR cc_start: 0.8412 (p) cc_final: 0.8136 (p) REVERT: C 30 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7720 (t) REVERT: C 41 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7012 (mm-30) REVERT: C 97 CYS cc_start: 0.5317 (p) cc_final: 0.4954 (p) REVERT: C 104 ASP cc_start: 0.7553 (t0) cc_final: 0.7220 (t0) REVERT: C 121 ILE cc_start: 0.8316 (mm) cc_final: 0.8084 (mt) REVERT: C 152 LYS cc_start: 0.8603 (mttm) cc_final: 0.8350 (mttm) REVERT: C 210 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6528 (mm-30) REVERT: C 253 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7252 (ttmm) REVERT: C 265 HIS cc_start: 0.7578 (t-90) cc_final: 0.7371 (t-90) REVERT: E 35 GLN cc_start: 0.7891 (tt0) cc_final: 0.7654 (tt0) REVERT: E 64 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7683 (t-90) REVERT: E 73 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6547 (t80) REVERT: E 79 GLU cc_start: 0.7333 (mp0) cc_final: 0.6825 (mp0) REVERT: E 81 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7855 (mmpt) REVERT: E 86 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7762 (t) REVERT: E 93 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7334 (mtp85) REVERT: E 150 VAL cc_start: 0.8601 (t) cc_final: 0.8229 (m) REVERT: E 155 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6926 (mt-10) REVERT: E 166 ARG cc_start: 0.7496 (mtm180) cc_final: 0.6841 (mtm180) REVERT: E 197 SER cc_start: 0.8484 (p) cc_final: 0.7944 (m) REVERT: F 124 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7633 (mt) REVERT: G 131 MET cc_start: -0.0329 (mtp) cc_final: -0.0672 (mtp) REVERT: G 137 ILE cc_start: 0.2245 (OUTLIER) cc_final: 0.1916 (mp) REVERT: H 7 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6397 (tm-30) REVERT: H 42 ASP cc_start: 0.7651 (m-30) cc_final: 0.7241 (m-30) REVERT: H 52 LEU cc_start: 0.8560 (tp) cc_final: 0.8285 (tt) REVERT: H 64 LEU cc_start: 0.8139 (mt) cc_final: 0.7759 (mt) REVERT: H 122 LEU cc_start: 0.8255 (mt) cc_final: 0.7582 (mt) REVERT: H 124 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7665 (ttt-90) REVERT: I 36 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7142 (mm) REVERT: I 46 GLN cc_start: 0.7978 (tt0) cc_final: 0.7464 (tm-30) REVERT: J 53 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (m) REVERT: J 62 TYR cc_start: 0.8147 (m-80) cc_final: 0.7839 (m-80) REVERT: K 23 LYS cc_start: 0.7685 (tptp) cc_final: 0.7147 (tptp) REVERT: K 50 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7971 (mp) REVERT: K 52 LYS cc_start: 0.8334 (mmtp) cc_final: 0.7896 (mmtp) REVERT: L 54 VAL cc_start: 0.8555 (t) cc_final: 0.8088 (m) REVERT: U 225 LEU cc_start: 0.7077 (mt) cc_final: 0.6839 (mt) REVERT: U 282 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6597 (mtm-85) REVERT: U 397 MET cc_start: 0.6626 (mtp) cc_final: 0.6101 (mtp) REVERT: U 510 LYS cc_start: 0.7512 (ptmm) cc_final: 0.7105 (ptmm) REVERT: U 555 ARG cc_start: 0.6948 (mtm110) cc_final: 0.6302 (mtm110) REVERT: U 598 LYS cc_start: 0.7567 (mttt) cc_final: 0.7177 (mttt) outliers start: 158 outliers final: 128 residues processed: 1002 average time/residue: 0.2543 time to fit residues: 391.4243 Evaluate side-chains 1054 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 908 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain A residue 1481 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1140 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 29 PHE Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 175 ARG Chi-restraints excluded: chain U residue 180 ARG Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 201 GLU Chi-restraints excluded: chain U residue 217 LYS Chi-restraints excluded: chain U residue 218 THR Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 274 GLN Chi-restraints excluded: chain U residue 282 ARG Chi-restraints excluded: chain U residue 340 MET Chi-restraints excluded: chain U residue 416 ILE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 526 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 384 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 387 optimal weight: 0.0570 chunk 327 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 423 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 321 optimal weight: 0.7980 chunk 366 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 861 GLN A1032 GLN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 113 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119021 restraints weight = 61627.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122727 restraints weight = 28555.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123314 restraints weight = 16335.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124382 restraints weight = 14362.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125434 restraints weight = 10414.849| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36662 Z= 0.145 Angle : 0.631 16.149 49742 Z= 0.315 Chirality : 0.045 0.249 5565 Planarity : 0.005 0.095 6258 Dihedral : 11.886 171.639 5471 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.85 % Favored : 93.95 % Rotamer: Outliers : 4.13 % Allowed : 21.32 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4314 helix: 1.11 (0.13), residues: 1594 sheet: -0.59 (0.21), residues: 603 loop : -1.06 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 118 TYR 0.020 0.001 TYR B 262 PHE 0.025 0.001 PHE C 38 TRP 0.015 0.001 TRP U 504 HIS 0.012 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00337 (36629) covalent geometry : angle 0.62325 (49695) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.25721 ( 2) hydrogen bonds : bond 0.03388 ( 1505) hydrogen bonds : angle 4.56770 ( 4231) metal coordination : bond 0.00687 ( 32) metal coordination : angle 3.27951 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8430.78 seconds wall clock time: 145 minutes 34.90 seconds (8734.90 seconds total)