Starting phenix.real_space_refine on Thu May 29 11:35:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehz_48071/05_2025/9ehz_48071.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 198 5.16 5 C 20132 2.51 5 N 5635 2.21 5 O 6105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32125 Number of models: 1 Model: "" Number of chains: 22 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} 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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "P" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} 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: "A" Number of atoms: 11392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1437, 11392 Classifications: {'peptide': 1437} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1367} Chain breaks: 3 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: "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: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5941 SG CYS I 17 42.202 103.105 137.790 1.00 57.19 S ATOM 5965 SG CYS I 20 45.807 103.834 136.631 1.00 48.34 S ATOM 6126 SG CYS I 39 44.937 100.292 137.485 1.00 62.17 S ATOM 6151 SG CYS I 42 44.911 102.899 140.225 1.00 54.74 S ATOM 6503 SG CYS I 86 13.343 100.469 105.189 1.00 59.58 S ATOM 6527 SG CYS I 89 11.993 104.000 104.189 1.00 67.85 S ATOM 6731 SG CYS I 114 15.130 102.525 102.605 1.00 69.25 S ATOM 6766 SG CYS I 119 15.049 103.741 106.181 1.00 69.63 S ATOM 6876 SG CYS J 7 49.943 95.614 40.336 1.00 17.86 S ATOM 6900 SG CYS J 10 48.945 94.206 36.920 1.00 35.61 S ATOM 7164 SG CYS J 44 46.780 93.634 40.173 1.00 31.69 S ATOM 7170 SG CYS J 45 46.940 96.850 38.139 1.00 42.85 S ATOM 8316 SG CYS L 19 78.967 123.588 56.330 1.00 54.83 S ATOM 8335 SG CYS L 22 78.701 126.870 54.349 1.00 47.43 S ATOM 8452 SG CYS L 36 82.111 125.316 55.083 1.00 72.44 S ATOM 8478 SG CYS L 39 80.123 126.850 57.843 1.00 70.68 S ATOM 10066 SG CYS A 71 108.637 78.834 79.984 1.00 51.66 S ATOM 10088 SG CYS A 74 108.290 75.294 78.521 1.00 45.37 S ATOM 10135 SG CYS A 81 105.211 77.653 78.707 1.00 52.86 S ATOM 10370 SG CYS A 111 94.461 68.324 124.320 1.00 67.00 S ATOM 10398 SG CYS A 114 97.520 66.101 123.966 1.00 68.53 S ATOM 10711 SG CYS A 154 93.925 64.755 124.965 1.00 86.11 S ATOM 10744 SG CYS A 184 96.187 66.356 127.389 1.00 92.84 S ATOM 29626 SG CYS B1119 106.666 62.175 88.178 1.00 60.91 S ATOM 29648 SG CYS B1122 104.528 64.497 90.411 1.00 57.07 S ATOM 29763 SG CYS B1137 107.654 65.744 88.740 1.00 54.35 S ATOM 29784 SG CYS B1140 107.781 63.355 91.735 1.00 59.13 S ATOM 30751 SG CYS C 88 76.761 91.990 19.916 1.00 65.52 S ATOM 30764 SG CYS C 90 79.161 94.300 21.831 1.00 67.48 S ATOM 30799 SG CYS C 94 76.782 95.647 19.281 1.00 53.85 S ATOM 30821 SG CYS C 97 75.427 94.453 22.600 1.00 54.81 S Time building chain proxies: 15.57, per 1000 atoms: 0.48 Number of scatterers: 32125 At special positions: 0 Unit cell: (169.05, 154.35, 164.85, 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 198 16.00 P 46 15.00 Mg 1 11.99 O 6105 8.00 N 5635 7.00 C 20132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.04 Conformation dependent library (CDL) restraints added in 4.0 seconds 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 154 " 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 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " 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 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " 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 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 45 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7350 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 47 sheets defined 37.7% alpha, 19.0% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 11.52 Creating SS restraints... Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.733A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.622A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.867A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.996A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 69 through 75 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: 3.689A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.982A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 109 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: 3.829A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 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 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 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: 3.764A 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 520 through 525 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.750A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (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: 3.995A 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 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.578A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.825A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.685A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.065A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.522A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) 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 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1119 through 1130 removed outlier: 3.871A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.972A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.623A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.604A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.971A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.916A 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 1453 through 1460 removed outlier: 3.834A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.545A 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 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.872A 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 324 removed outlier: 3.741A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 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: 3.616A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.533A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.668A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.143A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.680A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.606A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.108A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.783A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.826A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AA4, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.945A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.945A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 84 through 92 removed outlier: 7.239A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 117 through 120 removed outlier: 4.389A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.158A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'I' and resid 52 through 56 removed outlier: 6.403A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.804A pdb=" N LEU I 110 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 125 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'L' and resid 25 through 27 removed outlier: 6.770A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AB6, first strand: chain 'L' and resid 54 through 56 removed outlier: 5.033A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.385A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AB9, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.848A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.596A pdb=" N CYS A 111 " --> pdb=" O CYS A 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.080A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.801A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.624A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.795A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AC8, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.958A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AD2, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AD3, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AD4, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.615A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AD6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.217A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.686A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD9, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AE1, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.352A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AE3, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AE4, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.298A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE6, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.042A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE8, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.625A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1127 through 1129 removed outlier: 3.620A pdb=" N ASN B1129 " --> pdb=" O THR B1134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.596A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.327A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) 1357 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6269 1.33 - 1.45: 7921 1.45 - 1.58: 18229 1.58 - 1.70: 89 1.70 - 1.83: 314 Bond restraints: 32822 Sorted by residual: bond pdb=" C PRO A1098 " pdb=" O PRO A1098 " ideal model delta sigma weight residual 1.237 1.201 0.037 1.26e-02 6.30e+03 8.42e+00 bond pdb=" N THR A1103 " pdb=" CA THR A1103 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.08e-02 8.57e+03 8.09e+00 bond pdb=" C PRO A1122 " pdb=" O PRO A1122 " ideal model delta sigma weight residual 1.238 1.200 0.038 1.35e-02 5.49e+03 7.80e+00 bond pdb=" N TYR A1482 " pdb=" CA TYR A1482 " ideal model delta sigma weight residual 1.459 1.484 -0.025 9.10e-03 1.21e+04 7.64e+00 bond pdb=" C LYS A 346 " pdb=" N GLU A 347 " ideal model delta sigma weight residual 1.332 1.294 0.038 1.40e-02 5.10e+03 7.39e+00 ... (remaining 32817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 43770 2.44 - 4.88: 637 4.88 - 7.32: 109 7.32 - 9.76: 16 9.76 - 12.20: 3 Bond angle restraints: 44535 Sorted by residual: angle pdb=" N ASP E 46 " pdb=" CA ASP E 46 " pdb=" C ASP E 46 " ideal model delta sigma weight residual 108.67 117.31 -8.64 1.67e+00 3.59e-01 2.67e+01 angle pdb=" N THR B 836 " pdb=" CA THR B 836 " pdb=" C THR B 836 " ideal model delta sigma weight residual 114.75 108.29 6.46 1.26e+00 6.30e-01 2.63e+01 angle pdb=" C3' DC T 13 " pdb=" O3' DC T 13 " pdb=" P DG T 14 " ideal model delta sigma weight residual 120.20 127.76 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" C LYS A 853 " pdb=" CA LYS A 853 " pdb=" CB LYS A 853 " ideal model delta sigma weight residual 110.67 101.40 9.27 1.92e+00 2.71e-01 2.33e+01 angle pdb=" C ALA A 298 " pdb=" CA ALA A 298 " pdb=" CB ALA A 298 " ideal model delta sigma weight residual 115.79 110.17 5.62 1.19e+00 7.06e-01 2.23e+01 ... (remaining 44530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.73: 19356 30.73 - 61.47: 641 61.47 - 92.20: 40 92.20 - 122.94: 1 122.94 - 153.67: 4 Dihedral angle restraints: 20042 sinusoidal: 8677 harmonic: 11365 Sorted by residual: dihedral pdb=" CD ARG B 101 " pdb=" NE ARG B 101 " pdb=" CZ ARG B 101 " pdb=" NH1 ARG B 101 " ideal model delta sinusoidal sigma weight residual 0.00 77.46 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 146.08 33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CD ARG A1408 " pdb=" NE ARG A1408 " pdb=" CZ ARG A1408 " pdb=" NH1 ARG A1408 " ideal model delta sinusoidal sigma weight residual 0.00 -55.67 55.67 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 20039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4897 0.131 - 0.263: 37 0.263 - 0.394: 7 0.394 - 0.526: 23 0.526 - 0.657: 18 Chirality restraints: 4982 Sorted by residual: 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 -3.00 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DT N 15 " pdb=" OP1 DT N 15 " pdb=" OP2 DT N 15 " pdb=" O5' DT N 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DT T 2 " pdb=" OP1 DT T 2 " pdb=" OP2 DT T 2 " pdb=" O5' DT T 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.79e+00 ... (remaining 4979 not shown) Planarity restraints: 5619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 101 " -1.072 9.50e-02 1.11e+02 4.81e-01 1.39e+02 pdb=" NE ARG B 101 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B 101 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 101 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1408 " 0.894 9.50e-02 1.11e+02 4.01e-01 9.75e+01 pdb=" NE ARG A1408 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A1408 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A1408 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1408 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 172 " -0.673 9.50e-02 1.11e+02 3.01e-01 5.54e+01 pdb=" NE ARG E 172 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG E 172 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 172 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 172 " -0.021 2.00e-02 2.50e+03 ... (remaining 5616 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 15 2.17 - 2.85: 10825 2.85 - 3.53: 46030 3.53 - 4.22: 81133 4.22 - 4.90: 139673 Nonbonded interactions: 277676 Sorted by model distance: nonbonded pdb=" O3' C P 20 " pdb="MG MG P 101 " model vdw 1.481 2.170 nonbonded pdb=" O2 DC T 13 " pdb=" CB ALA A 855 " model vdw 1.532 3.460 nonbonded pdb=" O4 DT N 15 " pdb=" NZ LYS B 391 " model vdw 1.582 3.120 nonbonded pdb=" O4' DC T 15 " pdb=" OE1 GLN A 461 " model vdw 1.651 3.040 nonbonded pdb=" C1' DC T 15 " pdb=" OE1 GLN A 461 " model vdw 1.692 3.470 ... (remaining 277671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 82.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.130 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32854 Z= 0.233 Angle : 0.760 12.200 44580 Z= 0.433 Chirality : 0.066 0.657 4982 Planarity : 0.011 0.481 5619 Dihedral : 13.979 153.669 12692 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.01 % Favored : 94.73 % Rotamer: Outliers : 4.45 % Allowed : 6.60 % Favored : 88.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3870 helix: 1.34 (0.15), residues: 1329 sheet: 0.14 (0.22), residues: 590 loop : -0.51 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.005 0.001 HIS B 939 PHE 0.015 0.001 PHE A 548 TYR 0.016 0.001 TYR A 669 ARG 0.005 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.17898 ( 1384) hydrogen bonds : angle 7.01742 ( 3852) metal coordination : bond 0.00866 ( 32) metal coordination : angle 3.89357 ( 45) covalent geometry : bond 0.00449 (32822) covalent geometry : angle 0.75059 (44535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 972 time to evaluate : 3.376 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: D 20 LEU cc_start: 0.3278 (OUTLIER) cc_final: 0.2812 (tt) REVERT: E 5 GLU cc_start: 0.6879 (tp30) cc_final: 0.6585 (tp30) REVERT: E 9 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7771 (mtm-85) REVERT: E 100 THR cc_start: 0.8117 (p) cc_final: 0.7888 (t) REVERT: E 162 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8463 (tpt90) REVERT: H 11 ASP cc_start: 0.7691 (t0) cc_final: 0.7453 (t0) REVERT: H 62 SER cc_start: 0.9080 (p) cc_final: 0.8692 (m) REVERT: H 142 TYR cc_start: 0.8522 (m-80) cc_final: 0.8127 (m-80) REVERT: I 24 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8130 (mp) REVERT: J 1 MET cc_start: 0.8511 (tpp) cc_final: 0.8238 (ttm) REVERT: J 36 ASP cc_start: 0.8549 (m-30) cc_final: 0.8271 (m-30) REVERT: J 54 ASP cc_start: 0.8837 (t0) cc_final: 0.8610 (t70) REVERT: K 17 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8129 (mtpt) REVERT: K 36 ASN cc_start: 0.8449 (m110) cc_final: 0.7939 (m-40) REVERT: K 42 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8428 (mp) REVERT: K 70 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8206 (ttmm) REVERT: L 26 ASN cc_start: 0.7923 (p0) cc_final: 0.7700 (p0) REVERT: A 43 TYR cc_start: 0.8775 (m-80) cc_final: 0.8490 (m-80) REVERT: A 46 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8180 (m) REVERT: A 70 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7442 (mmm-85) REVERT: A 184 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6543 (p) REVERT: A 199 TYR cc_start: 0.8217 (m-80) cc_final: 0.7867 (m-80) REVERT: A 289 GLN cc_start: 0.8096 (tt0) cc_final: 0.7843 (tt0) REVERT: A 306 ASP cc_start: 0.8051 (m-30) cc_final: 0.7810 (m-30) REVERT: A 321 GLU cc_start: 0.7221 (tt0) cc_final: 0.6977 (tt0) REVERT: A 401 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8303 (ttm170) REVERT: A 418 TYR cc_start: 0.8532 (m-80) cc_final: 0.8296 (m-80) REVERT: A 485 ASN cc_start: 0.8103 (t0) cc_final: 0.7814 (t160) REVERT: A 516 GLN cc_start: 0.8368 (tt0) cc_final: 0.8145 (tt0) REVERT: A 687 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 697 LYS cc_start: 0.8375 (ttpp) cc_final: 0.7857 (tttp) REVERT: A 728 THR cc_start: 0.8463 (m) cc_final: 0.8051 (p) REVERT: A 740 GLN cc_start: 0.8665 (mt0) cc_final: 0.8354 (tt0) REVERT: A 742 ASN cc_start: 0.8585 (m-40) cc_final: 0.8314 (m110) REVERT: A 743 ARG cc_start: 0.7389 (ttp80) cc_final: 0.7017 (ttp80) REVERT: A 746 ASN cc_start: 0.8248 (m-40) cc_final: 0.8026 (m-40) REVERT: A 778 LYS cc_start: 0.8338 (mttt) cc_final: 0.8130 (mmmm) REVERT: A 787 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8742 (p) REVERT: A 845 GLU cc_start: 0.7898 (tt0) cc_final: 0.7640 (tt0) REVERT: A 849 ASP cc_start: 0.7475 (m-30) cc_final: 0.7182 (m-30) REVERT: A 868 MET cc_start: 0.8613 (mtm) cc_final: 0.8172 (mtm) REVERT: A 964 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7789 (mp0) REVERT: A 1155 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7795 (mptm) REVERT: A 1186 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7887 (m) REVERT: A 1196 TYR cc_start: 0.7025 (m-80) cc_final: 0.6386 (m-80) REVERT: A 1227 THR cc_start: 0.8694 (m) cc_final: 0.8363 (p) REVERT: A 1229 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6662 (tp30) REVERT: A 1230 GLN cc_start: 0.8302 (mt0) cc_final: 0.7909 (mt0) REVERT: A 1242 ASP cc_start: 0.7657 (p0) cc_final: 0.7355 (p0) REVERT: A 1261 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 1278 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6615 (tmmt) REVERT: A 1282 ASP cc_start: 0.7723 (t70) cc_final: 0.7417 (t70) REVERT: A 1284 PHE cc_start: 0.8676 (t80) cc_final: 0.8428 (t80) REVERT: A 1292 MET cc_start: 0.8225 (mtm) cc_final: 0.8017 (mtm) REVERT: A 1309 MET cc_start: 0.8285 (ttp) cc_final: 0.8079 (ttm) REVERT: A 1415 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8516 (p) REVERT: A 1428 MET cc_start: 0.7789 (tmm) cc_final: 0.7564 (tmm) REVERT: A 1441 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 1459 MET cc_start: 0.8466 (mtp) cc_final: 0.8262 (mtp) REVERT: B 53 MET cc_start: 0.8331 (mmm) cc_final: 0.8080 (mmm) REVERT: B 88 PHE cc_start: 0.7704 (m-80) cc_final: 0.7474 (m-80) REVERT: B 130 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8314 (ttpt) REVERT: B 409 LYS cc_start: 0.8333 (ttpp) cc_final: 0.8062 (ttpp) REVERT: B 439 ILE cc_start: 0.8023 (tt) cc_final: 0.7805 (mt) REVERT: B 537 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8196 (mm-40) REVERT: B 546 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 606 ASP cc_start: 0.8142 (t0) cc_final: 0.7807 (t0) REVERT: B 609 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 646 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7962 (ttm-80) REVERT: B 649 ASN cc_start: 0.8207 (t0) cc_final: 0.7949 (t0) REVERT: B 691 SER cc_start: 0.8743 (m) cc_final: 0.8458 (t) REVERT: B 728 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7876 (mtp) REVERT: B 826 GLU cc_start: 0.7440 (pt0) cc_final: 0.7231 (pt0) REVERT: B 844 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 896 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (mp) REVERT: B 1145 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: B 1172 MET cc_start: 0.8976 (mmm) cc_final: 0.8588 (mmp) REVERT: C 22 ILE cc_start: 0.8962 (mt) cc_final: 0.8714 (mt) REVERT: C 64 ILE cc_start: 0.8174 (pt) cc_final: 0.7971 (mt) REVERT: C 86 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8361 (ptt90) REVERT: C 104 ASP cc_start: 0.7768 (t0) cc_final: 0.7540 (t0) REVERT: C 160 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8144 (ttp-110) REVERT: C 162 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.8025 (ttp80) REVERT: C 207 GLU cc_start: 0.8052 (tt0) cc_final: 0.7706 (tt0) REVERT: C 260 GLN cc_start: 0.8288 (tt0) cc_final: 0.8024 (tt0) REVERT: C 266 GLU cc_start: 0.8070 (tp30) cc_final: 0.7799 (tp30) outliers start: 153 outliers final: 47 residues processed: 1056 average time/residue: 1.6030 time to fit residues: 1974.0816 Evaluate side-chains 888 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 825 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1263 ASN Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 100 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 304 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 ASN D 128 GLN E 189 GLN F 72 GLN G 9 HIS G 91 GLN H 87 GLN H 133 HIS I 45 GLN I 46 GLN I 67 GLN J 52 HIS K 2 ASN K 84 GLN L 26 ASN A 77 ASN A 152 ASN A 210 GLN A 278 HIS A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 780 ASN A 792 ASN A 861 GLN A 926 ASN A 949 GLN A1230 GLN A1244 ASN A1263 ASN A1299 GLN A1310 HIS A1462 GLN B 90 GLN B 143 GLN B 144 HIS B 197 GLN B 245 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 350 HIS B 410 ASN B 452 ASN B 585 ASN B 593 GLN B 639 HIS B 699 HIS B 717 ASN B 731 GLN B 817 GLN B 838 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 5 ASN C 32 ASN C 60 HIS C 114 HIS ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105838 restraints weight = 43772.215| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.75 r_work: 0.3290 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32854 Z= 0.164 Angle : 0.624 13.577 44580 Z= 0.320 Chirality : 0.046 0.207 4982 Planarity : 0.005 0.083 5619 Dihedral : 13.725 150.441 4938 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 4.97 % Allowed : 14.73 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3870 helix: 1.26 (0.15), residues: 1345 sheet: 0.18 (0.21), residues: 565 loop : -0.50 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.007 0.001 HIS B 939 PHE 0.020 0.002 PHE A 234 TYR 0.019 0.001 TYR A1176 ARG 0.009 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 1384) hydrogen bonds : angle 5.41316 ( 3852) metal coordination : bond 0.00763 ( 32) metal coordination : angle 4.64143 ( 45) covalent geometry : bond 0.00377 (32822) covalent geometry : angle 0.60629 (44535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 841 time to evaluate : 3.365 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: D 20 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3555 (tt) REVERT: D 48 ASN cc_start: 0.3327 (OUTLIER) cc_final: 0.2411 (t0) REVERT: E 5 GLU cc_start: 0.6991 (tp30) cc_final: 0.6663 (tp30) REVERT: E 100 THR cc_start: 0.8262 (p) cc_final: 0.8034 (t) REVERT: E 162 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8579 (tpt90) REVERT: G 2 PHE cc_start: 0.5809 (p90) cc_final: 0.5423 (p90) REVERT: G 77 PHE cc_start: 0.2784 (OUTLIER) cc_final: 0.2105 (t80) REVERT: G 104 MET cc_start: 0.4199 (mmm) cc_final: 0.3991 (tpp) REVERT: H 140 ARG cc_start: 0.8150 (mpt180) cc_final: 0.7867 (mpt180) REVERT: H 142 TYR cc_start: 0.8611 (m-80) cc_final: 0.8353 (m-80) REVERT: K 17 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8324 (mtpt) REVERT: K 106 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8364 (mtt-85) REVERT: L 44 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: A 43 TYR cc_start: 0.8866 (m-80) cc_final: 0.8585 (m-80) REVERT: A 70 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7723 (mmm-85) REVERT: A 132 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8170 (mmmm) REVERT: A 231 GLU cc_start: 0.7782 (mp0) cc_final: 0.7446 (mp0) REVERT: A 289 GLN cc_start: 0.8250 (tt0) cc_final: 0.8019 (tt0) REVERT: A 401 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8264 (ttm170) REVERT: A 403 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8401 (mm-40) REVERT: A 418 TYR cc_start: 0.8735 (m-80) cc_final: 0.8419 (m-80) REVERT: A 425 ASP cc_start: 0.8048 (p0) cc_final: 0.7684 (p0) REVERT: A 426 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7039 (mtt180) REVERT: A 556 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 687 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 697 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8013 (tttp) REVERT: A 728 THR cc_start: 0.8460 (m) cc_final: 0.8017 (p) REVERT: A 734 ARG cc_start: 0.7901 (mpp-170) cc_final: 0.7200 (mtt-85) REVERT: A 740 GLN cc_start: 0.8674 (mt0) cc_final: 0.8446 (mt0) REVERT: A 742 ASN cc_start: 0.8706 (m-40) cc_final: 0.8441 (m110) REVERT: A 743 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7502 (ttp80) REVERT: A 787 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 797 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8625 (mtm180) REVERT: A 845 GLU cc_start: 0.7998 (tt0) cc_final: 0.7696 (tt0) REVERT: A 849 ASP cc_start: 0.7474 (m-30) cc_final: 0.7212 (m-30) REVERT: A 868 MET cc_start: 0.8544 (mtm) cc_final: 0.7953 (mtm) REVERT: A 927 GLU cc_start: 0.7504 (tp30) cc_final: 0.7252 (tp30) REVERT: A 964 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8009 (mp0) REVERT: A 1008 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8295 (tttm) REVERT: A 1034 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7060 (tp40) REVERT: A 1155 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8028 (mttm) REVERT: A 1196 TYR cc_start: 0.7029 (m-80) cc_final: 0.6371 (m-80) REVERT: A 1242 ASP cc_start: 0.7714 (p0) cc_final: 0.7471 (p0) REVERT: A 1262 MET cc_start: 0.7883 (mtp) cc_final: 0.7489 (mtp) REVERT: A 1282 ASP cc_start: 0.7784 (t70) cc_final: 0.7558 (t70) REVERT: A 1284 PHE cc_start: 0.8711 (t80) cc_final: 0.8465 (t80) REVERT: A 1310 HIS cc_start: 0.8076 (p90) cc_final: 0.7627 (p-80) REVERT: A 1344 MET cc_start: 0.8206 (tpp) cc_final: 0.7973 (tpt) REVERT: A 1416 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8121 (ptp90) REVERT: B 84 TYR cc_start: 0.7654 (m-10) cc_final: 0.7354 (m-80) REVERT: B 130 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8533 (ttpt) REVERT: B 142 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 199 LYS cc_start: 0.8384 (ptmt) cc_final: 0.8178 (ptpt) REVERT: B 222 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7617 (mtp85) REVERT: B 255 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: B 297 MET cc_start: 0.8238 (ttp) cc_final: 0.7965 (mtp) REVERT: B 439 ILE cc_start: 0.8061 (tt) cc_final: 0.7853 (mt) REVERT: B 442 ASP cc_start: 0.7739 (m-30) cc_final: 0.7402 (m-30) REVERT: B 524 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8401 (mttp) REVERT: B 534 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 537 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8232 (mm-40) REVERT: B 551 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 606 ASP cc_start: 0.8082 (t0) cc_final: 0.7821 (t70) REVERT: B 646 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7790 (ttm-80) REVERT: B 649 ASN cc_start: 0.8284 (t0) cc_final: 0.7935 (t0) REVERT: B 691 SER cc_start: 0.8736 (m) cc_final: 0.8438 (t) REVERT: B 719 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 728 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: B 826 GLU cc_start: 0.7651 (pt0) cc_final: 0.7399 (pt0) REVERT: B 896 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 1172 MET cc_start: 0.9000 (mmm) cc_final: 0.8520 (mmt) REVERT: C 22 ILE cc_start: 0.9033 (mt) cc_final: 0.8832 (mt) REVERT: C 77 ASP cc_start: 0.7203 (m-30) cc_final: 0.6938 (m-30) REVERT: C 86 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8372 (ptt90) REVERT: C 104 ASP cc_start: 0.8024 (t0) cc_final: 0.7821 (t0) REVERT: C 126 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7834 (mtp180) REVERT: C 160 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8249 (ttp-110) REVERT: C 260 GLN cc_start: 0.8249 (tt0) cc_final: 0.7914 (tt0) REVERT: C 266 GLU cc_start: 0.8194 (tp30) cc_final: 0.7899 (tp30) outliers start: 171 outliers final: 81 residues processed: 930 average time/residue: 1.6363 time to fit residues: 1763.3933 Evaluate side-chains 888 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 790 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1416 ARG Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 155 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 341 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 19 GLN E 107 GLN E 132 GLN H 133 HIS I 45 GLN K 22 ASN K 84 GLN L 26 ASN A 204 HIS A 273 GLN A 293 ASN A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 673 GLN A 700 GLN A 757 GLN A1116 ASN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 312 GLN B 410 ASN B 486 ASN B 593 GLN B 980 HIS B1007 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104678 restraints weight = 43818.959| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.62 r_work: 0.3289 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32854 Z= 0.178 Angle : 0.606 12.727 44580 Z= 0.310 Chirality : 0.045 0.184 4982 Planarity : 0.004 0.070 5619 Dihedral : 13.439 149.862 4897 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 4.71 % Allowed : 17.35 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3870 helix: 1.26 (0.15), residues: 1339 sheet: 0.10 (0.22), residues: 558 loop : -0.60 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.013 0.001 HIS A1005 PHE 0.051 0.002 PHE E 73 TYR 0.018 0.001 TYR A 413 ARG 0.008 0.001 ARG F 100 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 1384) hydrogen bonds : angle 5.20811 ( 3852) metal coordination : bond 0.00797 ( 32) metal coordination : angle 4.53677 ( 45) covalent geometry : bond 0.00417 (32822) covalent geometry : angle 0.58867 (44535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 804 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3842 (OUTLIER) cc_final: 0.3440 (tt) REVERT: E 6 GLU cc_start: 0.8077 (tp30) cc_final: 0.7706 (tp30) REVERT: E 9 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7797 (mtt90) REVERT: E 33 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8609 (mt) REVERT: E 100 THR cc_start: 0.8315 (p) cc_final: 0.8040 (t) REVERT: E 132 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: E 162 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8593 (tpt90) REVERT: G 2 PHE cc_start: 0.6048 (p90) cc_final: 0.5751 (p90) REVERT: G 77 PHE cc_start: 0.2853 (OUTLIER) cc_final: 0.2128 (t80) REVERT: G 117 MET cc_start: 0.6343 (tmm) cc_final: 0.6090 (tpp) REVERT: H 24 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: H 140 ARG cc_start: 0.8172 (mpt180) cc_final: 0.7927 (mpt180) REVERT: H 142 TYR cc_start: 0.8736 (m-80) cc_final: 0.8382 (m-80) REVERT: I 80 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8194 (mtt-85) REVERT: K 29 ASN cc_start: 0.8535 (m-40) cc_final: 0.8307 (m-40) REVERT: L 26 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7625 (p0) REVERT: L 44 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: A 43 TYR cc_start: 0.8885 (m-80) cc_final: 0.8625 (m-80) REVERT: A 70 ARG cc_start: 0.8042 (mmt90) cc_final: 0.7681 (mmm-85) REVERT: A 132 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8182 (mmmm) REVERT: A 201 GLU cc_start: 0.7667 (tp30) cc_final: 0.7326 (mm-30) REVERT: A 231 GLU cc_start: 0.7760 (mp0) cc_final: 0.7424 (mp0) REVERT: A 289 GLN cc_start: 0.8235 (tt0) cc_final: 0.8003 (tt0) REVERT: A 321 GLU cc_start: 0.7439 (tt0) cc_final: 0.7184 (tt0) REVERT: A 401 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8222 (ttm170) REVERT: A 403 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8365 (mm-40) REVERT: A 418 TYR cc_start: 0.8734 (m-80) cc_final: 0.8432 (m-80) REVERT: A 423 ASN cc_start: 0.8073 (p0) cc_final: 0.7844 (p0) REVERT: A 426 ARG cc_start: 0.7337 (mtt180) cc_final: 0.7038 (mtt180) REVERT: A 728 THR cc_start: 0.8496 (m) cc_final: 0.8074 (p) REVERT: A 743 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7518 (ttp80) REVERT: A 845 GLU cc_start: 0.7944 (tt0) cc_final: 0.7649 (tt0) REVERT: A 849 ASP cc_start: 0.7469 (m-30) cc_final: 0.7194 (m-30) REVERT: A 868 MET cc_start: 0.8520 (mtm) cc_final: 0.8005 (mtm) REVERT: A 927 GLU cc_start: 0.7465 (tp30) cc_final: 0.7173 (tp30) REVERT: A 957 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 964 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8008 (mp0) REVERT: A 1008 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8315 (tttm) REVERT: A 1034 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7054 (tp40) REVERT: A 1155 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7957 (mmmm) REVERT: A 1196 TYR cc_start: 0.7072 (m-80) cc_final: 0.6380 (m-80) REVERT: A 1229 GLU cc_start: 0.7745 (tp30) cc_final: 0.7469 (tp30) REVERT: A 1242 ASP cc_start: 0.7748 (p0) cc_final: 0.7530 (p0) REVERT: A 1262 MET cc_start: 0.7823 (mtp) cc_final: 0.7525 (mtp) REVERT: A 1278 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6483 (tmmt) REVERT: A 1282 ASP cc_start: 0.7806 (t70) cc_final: 0.7569 (t70) REVERT: A 1292 MET cc_start: 0.8219 (mtm) cc_final: 0.7984 (mtm) REVERT: A 1344 MET cc_start: 0.8249 (tpp) cc_final: 0.7801 (tpt) REVERT: A 1416 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8148 (ptp90) REVERT: B 84 TYR cc_start: 0.7660 (m-10) cc_final: 0.7358 (m-80) REVERT: B 130 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8594 (ttpt) REVERT: B 255 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: B 260 LEU cc_start: 0.9027 (mp) cc_final: 0.8801 (mt) REVERT: B 297 MET cc_start: 0.8096 (ttp) cc_final: 0.7884 (mtp) REVERT: B 442 ASP cc_start: 0.7729 (m-30) cc_final: 0.7390 (m-30) REVERT: B 534 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8501 (t) REVERT: B 550 MET cc_start: 0.7559 (ttp) cc_final: 0.7160 (ttp) REVERT: B 551 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 606 ASP cc_start: 0.8074 (t0) cc_final: 0.7830 (t70) REVERT: B 649 ASN cc_start: 0.8294 (t0) cc_final: 0.7943 (t0) REVERT: B 691 SER cc_start: 0.8726 (m) cc_final: 0.8450 (t) REVERT: B 719 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 744 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: B 826 GLU cc_start: 0.7608 (pt0) cc_final: 0.7361 (pt0) REVERT: B 871 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7778 (m) REVERT: B 896 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 1026 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 1172 MET cc_start: 0.8971 (mmm) cc_final: 0.8626 (mmp) REVERT: C 77 ASP cc_start: 0.7195 (m-30) cc_final: 0.6981 (m-30) REVERT: C 86 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8376 (ptt90) REVERT: C 104 ASP cc_start: 0.8055 (t0) cc_final: 0.7851 (t0) REVERT: C 160 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8204 (ttp-110) REVERT: C 215 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: C 260 GLN cc_start: 0.8270 (tt0) cc_final: 0.7914 (tt0) outliers start: 162 outliers final: 85 residues processed: 883 average time/residue: 1.6608 time to fit residues: 1700.6558 Evaluate side-chains 879 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 778 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL 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 110 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1416 ARG Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 10 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 370 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 315 optimal weight: 0.5980 chunk 250 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 233 optimal weight: 0.3980 chunk 263 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 19 GLN E 107 GLN E 132 GLN E 133 GLN H 133 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 84 GLN L 26 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 410 ASN B 593 GLN B 825 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105436 restraints weight = 43883.952| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.64 r_work: 0.3300 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32854 Z= 0.140 Angle : 0.582 12.621 44580 Z= 0.297 Chirality : 0.044 0.172 4982 Planarity : 0.004 0.076 5619 Dihedral : 13.194 150.597 4890 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 4.71 % Allowed : 18.37 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3870 helix: 1.31 (0.14), residues: 1355 sheet: 0.07 (0.22), residues: 554 loop : -0.63 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.007 0.001 HIS A1005 PHE 0.020 0.001 PHE A 234 TYR 0.018 0.001 TYR A 413 ARG 0.008 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1384) hydrogen bonds : angle 5.05373 ( 3852) metal coordination : bond 0.00657 ( 32) metal coordination : angle 4.22197 ( 45) covalent geometry : bond 0.00324 (32822) covalent geometry : angle 0.56652 (44535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 799 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3809 (OUTLIER) cc_final: 0.3407 (tt) REVERT: E 6 GLU cc_start: 0.8058 (tp30) cc_final: 0.7643 (tp30) REVERT: E 9 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7847 (mtt90) REVERT: E 73 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7581 (t80) REVERT: E 100 THR cc_start: 0.8333 (p) cc_final: 0.8081 (t) REVERT: E 162 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8606 (tpt90) REVERT: F 83 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7943 (pp) REVERT: G 2 PHE cc_start: 0.6167 (p90) cc_final: 0.5770 (p90) REVERT: G 12 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8566 (mm) REVERT: G 77 PHE cc_start: 0.2670 (OUTLIER) cc_final: 0.2014 (t80) REVERT: H 24 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8298 (mtm-85) REVERT: H 140 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7847 (mpt180) REVERT: H 142 TYR cc_start: 0.8827 (m-80) cc_final: 0.8368 (m-80) REVERT: I 80 ARG cc_start: 0.8502 (ptp-170) cc_final: 0.8067 (mtt90) REVERT: K 29 ASN cc_start: 0.8526 (m-40) cc_final: 0.8296 (m-40) REVERT: L 44 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: A 43 TYR cc_start: 0.8889 (m-80) cc_final: 0.8620 (m-80) REVERT: A 70 ARG cc_start: 0.8065 (mmt90) cc_final: 0.7699 (mmm-85) REVERT: A 116 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7957 (mtpm) REVERT: A 201 GLU cc_start: 0.7725 (tp30) cc_final: 0.7284 (mm-30) REVERT: A 266 MET cc_start: 0.3182 (mmm) cc_final: 0.2954 (mmm) REVERT: A 289 GLN cc_start: 0.8246 (tt0) cc_final: 0.7998 (tt0) REVERT: A 290 LEU cc_start: 0.8802 (tp) cc_final: 0.8514 (tp) REVERT: A 321 GLU cc_start: 0.7420 (tt0) cc_final: 0.7104 (tt0) REVERT: A 382 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7733 (ttp-110) REVERT: A 403 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8342 (mm-40) REVERT: A 418 TYR cc_start: 0.8680 (m-80) cc_final: 0.8445 (m-80) REVERT: A 423 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7877 (p0) REVERT: A 728 THR cc_start: 0.8483 (m) cc_final: 0.8078 (p) REVERT: A 743 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7496 (ttp80) REVERT: A 845 GLU cc_start: 0.7950 (tt0) cc_final: 0.7662 (tt0) REVERT: A 849 ASP cc_start: 0.7501 (m-30) cc_final: 0.7249 (m-30) REVERT: A 868 MET cc_start: 0.8490 (mtm) cc_final: 0.8062 (mtm) REVERT: A 927 GLU cc_start: 0.7401 (tp30) cc_final: 0.7192 (tp30) REVERT: A 964 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8021 (mp0) REVERT: A 1008 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8327 (tttm) REVERT: A 1034 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7052 (tp40) REVERT: A 1177 TYR cc_start: 0.8213 (t80) cc_final: 0.7816 (t80) REVERT: A 1196 TYR cc_start: 0.7093 (m-80) cc_final: 0.6339 (m-80) REVERT: A 1229 GLU cc_start: 0.7715 (tp30) cc_final: 0.7370 (tp30) REVERT: A 1262 MET cc_start: 0.7838 (mtp) cc_final: 0.7531 (mtp) REVERT: A 1282 ASP cc_start: 0.7786 (t70) cc_final: 0.7541 (t70) REVERT: A 1292 MET cc_start: 0.8180 (mtm) cc_final: 0.7955 (mtm) REVERT: B 130 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8574 (ttpt) REVERT: B 255 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7557 (mmm-85) REVERT: B 297 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7842 (mtp) REVERT: B 301 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 442 ASP cc_start: 0.7738 (m-30) cc_final: 0.7390 (m-30) REVERT: B 534 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 551 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 606 ASP cc_start: 0.8079 (t0) cc_final: 0.7838 (t70) REVERT: B 649 ASN cc_start: 0.8235 (t0) cc_final: 0.7868 (t0) REVERT: B 691 SER cc_start: 0.8725 (m) cc_final: 0.8446 (t) REVERT: B 719 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (p) REVERT: B 744 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7494 (mmm) REVERT: B 796 MET cc_start: 0.8654 (mtp) cc_final: 0.8445 (mtt) REVERT: B 826 GLU cc_start: 0.7619 (pt0) cc_final: 0.7397 (pt0) REVERT: B 866 ILE cc_start: 0.7731 (mm) cc_final: 0.7438 (mp) REVERT: B 896 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 1171 MET cc_start: 0.8894 (mtm) cc_final: 0.8688 (mtp) REVERT: B 1172 MET cc_start: 0.8965 (mmm) cc_final: 0.8482 (mmt) REVERT: C 18 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 86 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8387 (ptt90) REVERT: C 100 GLU cc_start: 0.8161 (tt0) cc_final: 0.7912 (tt0) REVERT: C 160 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8189 (ttp-110) REVERT: C 211 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7839 (pp) REVERT: C 215 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: C 258 ASP cc_start: 0.8280 (m-30) cc_final: 0.8059 (m-30) REVERT: C 260 GLN cc_start: 0.8239 (tt0) cc_final: 0.7881 (tt0) outliers start: 162 outliers final: 94 residues processed: 885 average time/residue: 1.6384 time to fit residues: 1683.0556 Evaluate side-chains 895 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 781 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 58 MET 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 110 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 122 optimal weight: 0.0980 chunk 361 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 88 optimal weight: 0.0040 chunk 348 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 273 optimal weight: 0.6980 chunk 321 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 84 GLN L 26 ASN A 152 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 410 ASN B 593 GLN B 825 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 177 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108937 restraints weight = 43757.312| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.61 r_work: 0.3321 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32854 Z= 0.121 Angle : 0.567 12.298 44580 Z= 0.290 Chirality : 0.044 0.191 4982 Planarity : 0.004 0.062 5619 Dihedral : 13.000 151.267 4888 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.09 % Favored : 94.65 % Rotamer: Outliers : 4.80 % Allowed : 18.92 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3870 helix: 1.42 (0.15), residues: 1344 sheet: 0.06 (0.22), residues: 564 loop : -0.66 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.006 0.001 HIS A1005 PHE 0.011 0.001 PHE B1108 TYR 0.016 0.001 TYR A 413 ARG 0.010 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1384) hydrogen bonds : angle 4.91514 ( 3852) metal coordination : bond 0.00536 ( 32) metal coordination : angle 4.11014 ( 45) covalent geometry : bond 0.00275 (32822) covalent geometry : angle 0.55180 (44535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 803 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3795 (OUTLIER) cc_final: 0.3403 (tt) REVERT: E 6 GLU cc_start: 0.8036 (tp30) cc_final: 0.7617 (tp30) REVERT: E 100 THR cc_start: 0.8351 (p) cc_final: 0.8095 (t) REVERT: E 162 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8513 (tpt170) REVERT: F 83 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7925 (pp) REVERT: G 12 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mm) REVERT: G 77 PHE cc_start: 0.2628 (OUTLIER) cc_final: 0.1996 (t80) REVERT: H 42 ASP cc_start: 0.8097 (m-30) cc_final: 0.7735 (m-30) REVERT: H 98 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8206 (ttt180) REVERT: H 142 TYR cc_start: 0.8830 (m-80) cc_final: 0.8328 (m-80) REVERT: I 40 ARG cc_start: 0.8379 (mtt-85) cc_final: 0.8177 (mtt-85) REVERT: I 80 ARG cc_start: 0.8456 (ptp-170) cc_final: 0.8111 (mtt-85) REVERT: K 29 ASN cc_start: 0.8530 (m-40) cc_final: 0.8279 (m-40) REVERT: L 26 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7433 (p0) REVERT: L 44 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: A 116 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7768 (mtpp) REVERT: A 201 GLU cc_start: 0.7708 (tp30) cc_final: 0.7400 (mm-30) REVERT: A 266 MET cc_start: 0.3295 (mmm) cc_final: 0.3047 (mmm) REVERT: A 289 GLN cc_start: 0.8230 (tt0) cc_final: 0.8019 (tt0) REVERT: A 290 LEU cc_start: 0.8794 (tp) cc_final: 0.8500 (tp) REVERT: A 321 GLU cc_start: 0.7439 (tt0) cc_final: 0.7116 (tt0) REVERT: A 382 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7751 (ttp-110) REVERT: A 418 TYR cc_start: 0.8643 (m-80) cc_final: 0.8401 (m-80) REVERT: A 728 THR cc_start: 0.8479 (m) cc_final: 0.8083 (p) REVERT: A 743 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7497 (ttp80) REVERT: A 845 GLU cc_start: 0.7922 (tt0) cc_final: 0.7643 (tt0) REVERT: A 849 ASP cc_start: 0.7498 (m-30) cc_final: 0.7245 (m-30) REVERT: A 868 MET cc_start: 0.8471 (mtm) cc_final: 0.8033 (mtm) REVERT: A 927 GLU cc_start: 0.7351 (tp30) cc_final: 0.7141 (tp30) REVERT: A 964 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8033 (mp0) REVERT: A 1008 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8331 (tttm) REVERT: A 1042 ASN cc_start: 0.8543 (m-40) cc_final: 0.8286 (m-40) REVERT: A 1196 TYR cc_start: 0.7105 (m-80) cc_final: 0.6304 (m-80) REVERT: A 1229 GLU cc_start: 0.7677 (tp30) cc_final: 0.7270 (tp30) REVERT: A 1262 MET cc_start: 0.7811 (mtp) cc_final: 0.7487 (mtp) REVERT: A 1282 ASP cc_start: 0.7739 (t70) cc_final: 0.7507 (t70) REVERT: A 1287 CYS cc_start: 0.8150 (t) cc_final: 0.7921 (m) REVERT: A 1292 MET cc_start: 0.8144 (mtm) cc_final: 0.7912 (mtm) REVERT: A 1344 MET cc_start: 0.8145 (tpt) cc_final: 0.7882 (tpp) REVERT: B 130 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8544 (ttpt) REVERT: B 223 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (m) REVERT: B 255 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: B 301 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 320 PHE cc_start: 0.8597 (t80) cc_final: 0.8210 (t80) REVERT: B 323 SER cc_start: 0.8737 (t) cc_final: 0.8465 (p) REVERT: B 324 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6134 (mtm-85) REVERT: B 442 ASP cc_start: 0.7728 (m-30) cc_final: 0.7388 (m-30) REVERT: B 534 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8447 (t) REVERT: B 551 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 606 ASP cc_start: 0.8123 (t0) cc_final: 0.7877 (t0) REVERT: B 649 ASN cc_start: 0.8158 (t0) cc_final: 0.7803 (t0) REVERT: B 691 SER cc_start: 0.8701 (m) cc_final: 0.8426 (t) REVERT: B 744 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7413 (mmm) REVERT: B 826 GLU cc_start: 0.7563 (pt0) cc_final: 0.7292 (pt0) REVERT: B 866 ILE cc_start: 0.7710 (mm) cc_final: 0.7451 (mp) REVERT: B 896 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7846 (mp) REVERT: B 1026 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 1165 MET cc_start: 0.8515 (mtm) cc_final: 0.8314 (mtp) REVERT: B 1171 MET cc_start: 0.8914 (mtm) cc_final: 0.8709 (mtp) REVERT: B 1172 MET cc_start: 0.8959 (mmm) cc_final: 0.8450 (mmt) REVERT: C 18 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7709 (t0) REVERT: C 86 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8380 (ptt90) REVERT: C 162 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8281 (ttp80) REVERT: C 211 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7659 (pp) REVERT: C 260 GLN cc_start: 0.8227 (tt0) cc_final: 0.7866 (tt0) outliers start: 165 outliers final: 91 residues processed: 879 average time/residue: 1.6906 time to fit residues: 1722.7272 Evaluate side-chains 892 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 784 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG 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 G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain A residue 58 MET 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 116 LYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 382 optimal weight: 0.4980 chunk 264 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 274 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 297 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 226 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 107 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 84 GLN L 26 ASN A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 410 ASN B 582 GLN B 593 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108704 restraints weight = 43888.220| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.62 r_work: 0.3316 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32854 Z= 0.131 Angle : 0.577 12.718 44580 Z= 0.294 Chirality : 0.044 0.237 4982 Planarity : 0.004 0.069 5619 Dihedral : 12.856 149.780 4876 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.06 % Favored : 94.68 % Rotamer: Outliers : 4.24 % Allowed : 20.20 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3870 helix: 1.47 (0.15), residues: 1339 sheet: 0.05 (0.22), residues: 560 loop : -0.66 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.005 0.001 HIS A1005 PHE 0.022 0.001 PHE A 234 TYR 0.016 0.001 TYR A 413 ARG 0.009 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 1384) hydrogen bonds : angle 4.87492 ( 3852) metal coordination : bond 0.00548 ( 32) metal coordination : angle 4.13256 ( 45) covalent geometry : bond 0.00301 (32822) covalent geometry : angle 0.56235 (44535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 792 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3439 (tt) REVERT: E 5 GLU cc_start: 0.6966 (tp30) cc_final: 0.6698 (tp30) REVERT: E 9 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7610 (mtt90) REVERT: E 18 MET cc_start: 0.8915 (mmt) cc_final: 0.8705 (mmm) REVERT: E 100 THR cc_start: 0.8345 (p) cc_final: 0.8105 (t) REVERT: E 162 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8477 (tpt90) REVERT: G 12 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8510 (mm) REVERT: G 77 PHE cc_start: 0.2780 (OUTLIER) cc_final: 0.2119 (t80) REVERT: H 42 ASP cc_start: 0.8124 (m-30) cc_final: 0.7810 (m-30) REVERT: H 142 TYR cc_start: 0.8840 (m-80) cc_final: 0.8357 (m-80) REVERT: I 80 ARG cc_start: 0.8436 (ptp-170) cc_final: 0.8110 (mtt-85) REVERT: J 24 LEU cc_start: 0.8426 (mt) cc_final: 0.8146 (mp) REVERT: J 48 MET cc_start: 0.8890 (mmm) cc_final: 0.8646 (mmm) REVERT: K 29 ASN cc_start: 0.8519 (m-40) cc_final: 0.8277 (m-40) REVERT: L 26 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7628 (p0) REVERT: L 44 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: A 116 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7749 (mtpp) REVERT: A 139 LYS cc_start: 0.8291 (mtpp) cc_final: 0.8086 (ttmm) REVERT: A 201 GLU cc_start: 0.7721 (tp30) cc_final: 0.7421 (mm-30) REVERT: A 266 MET cc_start: 0.3338 (mmm) cc_final: 0.3102 (mmm) REVERT: A 274 ASP cc_start: 0.8124 (t0) cc_final: 0.7863 (t0) REVERT: A 289 GLN cc_start: 0.8240 (tt0) cc_final: 0.8021 (tt0) REVERT: A 290 LEU cc_start: 0.8787 (tp) cc_final: 0.8493 (tp) REVERT: A 321 GLU cc_start: 0.7416 (tt0) cc_final: 0.7088 (tt0) REVERT: A 382 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7733 (ttp-110) REVERT: A 418 TYR cc_start: 0.8628 (m-80) cc_final: 0.8411 (m-80) REVERT: A 728 THR cc_start: 0.8470 (m) cc_final: 0.8082 (p) REVERT: A 740 GLN cc_start: 0.8674 (mt0) cc_final: 0.8464 (tt0) REVERT: A 783 GLN cc_start: 0.8484 (mt0) cc_final: 0.8272 (mt0) REVERT: A 845 GLU cc_start: 0.7923 (tt0) cc_final: 0.7630 (tt0) REVERT: A 849 ASP cc_start: 0.7482 (m-30) cc_final: 0.7220 (m-30) REVERT: A 868 MET cc_start: 0.8469 (mtm) cc_final: 0.8024 (mtm) REVERT: A 927 GLU cc_start: 0.7345 (tp30) cc_final: 0.7133 (tp30) REVERT: A 964 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8001 (mp0) REVERT: A 1008 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8345 (tttm) REVERT: A 1034 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.6976 (tp40) REVERT: A 1042 ASN cc_start: 0.8520 (m-40) cc_final: 0.8245 (m-40) REVERT: A 1155 LYS cc_start: 0.8222 (tptm) cc_final: 0.7955 (mptm) REVERT: A 1196 TYR cc_start: 0.7096 (m-80) cc_final: 0.6281 (m-80) REVERT: A 1229 GLU cc_start: 0.7589 (tp30) cc_final: 0.7088 (tp30) REVERT: A 1262 MET cc_start: 0.7815 (mtp) cc_final: 0.7485 (mtp) REVERT: A 1282 ASP cc_start: 0.7719 (t70) cc_final: 0.7495 (t70) REVERT: A 1287 CYS cc_start: 0.8167 (t) cc_final: 0.7962 (m) REVERT: B 52 GLN cc_start: 0.8136 (mt0) cc_final: 0.7875 (mt0) REVERT: B 130 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8534 (ttpt) REVERT: B 155 MET cc_start: 0.8757 (ttm) cc_final: 0.8293 (ttp) REVERT: B 223 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8262 (m) REVERT: B 255 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7557 (mmm-85) REVERT: B 301 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 320 PHE cc_start: 0.8573 (t80) cc_final: 0.8212 (t80) REVERT: B 323 SER cc_start: 0.8745 (t) cc_final: 0.8473 (p) REVERT: B 324 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6113 (mtm-85) REVERT: B 442 ASP cc_start: 0.7626 (m-30) cc_final: 0.7287 (m-30) REVERT: B 551 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7369 (mt-10) REVERT: B 606 ASP cc_start: 0.8127 (t0) cc_final: 0.7837 (t0) REVERT: B 649 ASN cc_start: 0.8156 (t0) cc_final: 0.7783 (t0) REVERT: B 691 SER cc_start: 0.8701 (m) cc_final: 0.8422 (t) REVERT: B 744 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7519 (mmm) REVERT: B 826 GLU cc_start: 0.7585 (pt0) cc_final: 0.7332 (pt0) REVERT: B 896 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 1026 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 1171 MET cc_start: 0.8979 (mtm) cc_final: 0.8755 (mtp) REVERT: C 13 GLU cc_start: 0.8042 (tt0) cc_final: 0.7696 (tt0) REVERT: C 86 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8408 (ptt90) REVERT: C 211 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (pp) REVERT: C 258 ASP cc_start: 0.8275 (m-30) cc_final: 0.8069 (m-30) REVERT: C 260 GLN cc_start: 0.8222 (tt0) cc_final: 0.7836 (tt0) outliers start: 146 outliers final: 96 residues processed: 863 average time/residue: 1.7607 time to fit residues: 1786.3439 Evaluate side-chains 889 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 778 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain A residue 58 MET 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 116 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 191 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 344 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 84 GLN L 26 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 410 ASN B 582 GLN B 593 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107746 restraints weight = 43853.641| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.81 r_work: 0.3280 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32854 Z= 0.158 Angle : 0.594 12.709 44580 Z= 0.301 Chirality : 0.045 0.213 4982 Planarity : 0.004 0.062 5619 Dihedral : 12.781 146.666 4876 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.63 % Rotamer: Outliers : 4.27 % Allowed : 20.52 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3870 helix: 1.41 (0.14), residues: 1347 sheet: -0.06 (0.21), residues: 567 loop : -0.68 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.005 0.001 HIS A1005 PHE 0.013 0.001 PHE B 88 TYR 0.016 0.001 TYR A 413 ARG 0.010 0.001 ARG A 960 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1384) hydrogen bonds : angle 4.90020 ( 3852) metal coordination : bond 0.00683 ( 32) metal coordination : angle 4.30939 ( 45) covalent geometry : bond 0.00371 (32822) covalent geometry : angle 0.57861 (44535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 804 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3601 (tt) REVERT: E 5 GLU cc_start: 0.7127 (tp30) cc_final: 0.6832 (tp30) REVERT: E 9 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7739 (mtt90) REVERT: E 100 THR cc_start: 0.8375 (p) cc_final: 0.8111 (t) REVERT: E 162 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8543 (tpt90) REVERT: G 12 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8535 (mm) REVERT: G 77 PHE cc_start: 0.2820 (OUTLIER) cc_final: 0.2127 (t80) REVERT: G 117 MET cc_start: 0.6862 (tmm) cc_final: 0.5826 (tpp) REVERT: H 42 ASP cc_start: 0.8156 (m-30) cc_final: 0.7838 (m-30) REVERT: H 142 TYR cc_start: 0.8899 (m-80) cc_final: 0.8399 (m-80) REVERT: I 80 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8179 (mtt-85) REVERT: J 24 LEU cc_start: 0.8452 (mt) cc_final: 0.8168 (mp) REVERT: K 29 ASN cc_start: 0.8565 (m-40) cc_final: 0.8318 (m-40) REVERT: L 26 ASN cc_start: 0.8211 (p0) cc_final: 0.7706 (p0) REVERT: L 44 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7994 (mtp) REVERT: A 116 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7812 (mtpp) REVERT: A 201 GLU cc_start: 0.7715 (tp30) cc_final: 0.7371 (mm-30) REVERT: A 266 MET cc_start: 0.3391 (mmm) cc_final: 0.3159 (mmm) REVERT: A 274 ASP cc_start: 0.8150 (t0) cc_final: 0.7915 (t0) REVERT: A 289 GLN cc_start: 0.8280 (tt0) cc_final: 0.8025 (tt0) REVERT: A 290 LEU cc_start: 0.8787 (tp) cc_final: 0.8484 (tp) REVERT: A 321 GLU cc_start: 0.7503 (tt0) cc_final: 0.7158 (tt0) REVERT: A 382 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7772 (ttp-110) REVERT: A 418 TYR cc_start: 0.8639 (m-80) cc_final: 0.8422 (m-80) REVERT: A 728 THR cc_start: 0.8490 (m) cc_final: 0.8099 (p) REVERT: A 783 GLN cc_start: 0.8530 (mt0) cc_final: 0.8316 (mt0) REVERT: A 845 GLU cc_start: 0.7985 (tt0) cc_final: 0.7716 (tt0) REVERT: A 849 ASP cc_start: 0.7535 (m-30) cc_final: 0.7264 (m-30) REVERT: A 868 MET cc_start: 0.8485 (mtm) cc_final: 0.8033 (mtm) REVERT: A 927 GLU cc_start: 0.7397 (tp30) cc_final: 0.7174 (tp30) REVERT: A 964 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8064 (mp0) REVERT: A 1008 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8364 (tttm) REVERT: A 1034 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.6994 (tp40) REVERT: A 1042 ASN cc_start: 0.8544 (m-40) cc_final: 0.8287 (m-40) REVERT: A 1102 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7380 (mtt) REVERT: A 1195 VAL cc_start: 0.7922 (t) cc_final: 0.7699 (m) REVERT: A 1196 TYR cc_start: 0.7233 (m-80) cc_final: 0.6386 (m-80) REVERT: A 1229 GLU cc_start: 0.7661 (tp30) cc_final: 0.7453 (tp30) REVERT: A 1262 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: A 1282 ASP cc_start: 0.7783 (t70) cc_final: 0.7556 (t70) REVERT: B 88 PHE cc_start: 0.7746 (m-80) cc_final: 0.7423 (m-80) REVERT: B 130 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8540 (ttpt) REVERT: B 155 MET cc_start: 0.8619 (ttm) cc_final: 0.8322 (ttp) REVERT: B 223 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8288 (m) REVERT: B 255 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7540 (mmm-85) REVERT: B 301 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8006 (p) REVERT: B 320 PHE cc_start: 0.8533 (t80) cc_final: 0.8141 (t80) REVERT: B 323 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 324 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6111 (mtm-85) REVERT: B 442 ASP cc_start: 0.7697 (m-30) cc_final: 0.7348 (m-30) REVERT: B 551 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 606 ASP cc_start: 0.8165 (t0) cc_final: 0.7910 (t0) REVERT: B 646 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: B 649 ASN cc_start: 0.8228 (t0) cc_final: 0.7824 (t0) REVERT: B 691 SER cc_start: 0.8719 (m) cc_final: 0.8433 (t) REVERT: B 744 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7735 (mmm) REVERT: B 812 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8217 (ttm-80) REVERT: B 826 GLU cc_start: 0.7660 (pt0) cc_final: 0.7357 (pt0) REVERT: B 896 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 1026 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 1171 MET cc_start: 0.9001 (mtm) cc_final: 0.8759 (mtp) REVERT: C 18 ASN cc_start: 0.8663 (p0) cc_final: 0.8361 (p0) REVERT: C 86 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8423 (ptt90) REVERT: C 258 ASP cc_start: 0.8291 (m-30) cc_final: 0.8082 (m-30) REVERT: C 260 GLN cc_start: 0.8268 (tt0) cc_final: 0.7897 (tt0) outliers start: 147 outliers final: 96 residues processed: 870 average time/residue: 1.6946 time to fit residues: 1704.5855 Evaluate side-chains 900 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 788 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL 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 116 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 95 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 303 optimal weight: 0.2980 chunk 107 optimal weight: 0.0470 chunk 194 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 296 optimal weight: 0.0670 chunk 217 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 36 ASN K 84 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 468 GLN B 582 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109668 restraints weight = 43957.875| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.62 r_work: 0.3332 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32854 Z= 0.117 Angle : 0.583 12.842 44580 Z= 0.294 Chirality : 0.043 0.220 4982 Planarity : 0.004 0.065 5619 Dihedral : 12.643 146.346 4874 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.01 % Favored : 94.73 % Rotamer: Outliers : 3.43 % Allowed : 21.62 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3870 helix: 1.52 (0.15), residues: 1339 sheet: 0.02 (0.22), residues: 550 loop : -0.67 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.005 0.001 HIS B 939 PHE 0.023 0.001 PHE A 234 TYR 0.016 0.001 TYR A 413 ARG 0.009 0.000 ARG A 960 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 1384) hydrogen bonds : angle 4.80337 ( 3852) metal coordination : bond 0.00458 ( 32) metal coordination : angle 4.01489 ( 45) covalent geometry : bond 0.00266 (32822) covalent geometry : angle 0.56936 (44535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 794 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3941 (OUTLIER) cc_final: 0.3593 (tt) REVERT: E 5 GLU cc_start: 0.6966 (tp30) cc_final: 0.6583 (tp30) REVERT: E 18 MET cc_start: 0.8917 (mmt) cc_final: 0.8666 (mmm) REVERT: E 100 THR cc_start: 0.8327 (p) cc_final: 0.8077 (t) REVERT: E 162 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8553 (tpt170) REVERT: E 181 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8264 (mtm110) REVERT: G 12 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8466 (mm) REVERT: G 77 PHE cc_start: 0.2720 (OUTLIER) cc_final: 0.2061 (t80) REVERT: G 145 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6724 (tt) REVERT: H 42 ASP cc_start: 0.8097 (m-30) cc_final: 0.7795 (m-30) REVERT: H 142 TYR cc_start: 0.8869 (m-80) cc_final: 0.8337 (m-80) REVERT: I 40 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.8057 (mtt-85) REVERT: I 80 ARG cc_start: 0.8420 (ptp-170) cc_final: 0.8131 (mtt-85) REVERT: J 24 LEU cc_start: 0.8440 (mt) cc_final: 0.8165 (mp) REVERT: K 29 ASN cc_start: 0.8549 (m-40) cc_final: 0.8303 (m-40) REVERT: L 26 ASN cc_start: 0.8179 (p0) cc_final: 0.7648 (p0) REVERT: L 44 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7964 (mtp) REVERT: A 116 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7681 (mtpp) REVERT: A 151 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7631 (mtmm) REVERT: A 201 GLU cc_start: 0.7660 (tp30) cc_final: 0.7367 (mm-30) REVERT: A 266 MET cc_start: 0.3414 (mmm) cc_final: 0.3180 (mmm) REVERT: A 274 ASP cc_start: 0.8084 (t0) cc_final: 0.7867 (t0) REVERT: A 289 GLN cc_start: 0.8237 (tt0) cc_final: 0.8006 (tt0) REVERT: A 290 LEU cc_start: 0.8759 (tp) cc_final: 0.8484 (tp) REVERT: A 321 GLU cc_start: 0.7530 (tt0) cc_final: 0.7202 (tt0) REVERT: A 382 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7706 (ttp-110) REVERT: A 401 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8186 (ttm170) REVERT: A 418 TYR cc_start: 0.8574 (m-80) cc_final: 0.8373 (m-80) REVERT: A 728 THR cc_start: 0.8462 (m) cc_final: 0.8070 (p) REVERT: A 742 ASN cc_start: 0.8718 (m-40) cc_final: 0.8454 (m110) REVERT: A 783 GLN cc_start: 0.8486 (mt0) cc_final: 0.8279 (mt0) REVERT: A 845 GLU cc_start: 0.7897 (tt0) cc_final: 0.7614 (tt0) REVERT: A 849 ASP cc_start: 0.7496 (m-30) cc_final: 0.7227 (m-30) REVERT: A 868 MET cc_start: 0.8443 (mtm) cc_final: 0.8005 (mtm) REVERT: A 927 GLU cc_start: 0.7273 (tp30) cc_final: 0.7055 (tp30) REVERT: A 964 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7987 (mp0) REVERT: A 1008 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8333 (tttm) REVERT: A 1034 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.6999 (tp40) REVERT: A 1042 ASN cc_start: 0.8464 (m-40) cc_final: 0.8231 (m-40) REVERT: A 1149 ARG cc_start: 0.8467 (mtm110) cc_final: 0.7814 (mtm-85) REVERT: A 1195 VAL cc_start: 0.7841 (t) cc_final: 0.7627 (m) REVERT: A 1196 TYR cc_start: 0.7188 (m-80) cc_final: 0.6303 (m-80) REVERT: A 1229 GLU cc_start: 0.7534 (tp30) cc_final: 0.7321 (tp30) REVERT: A 1257 LEU cc_start: 0.8421 (tt) cc_final: 0.8152 (tp) REVERT: A 1262 MET cc_start: 0.7806 (mtp) cc_final: 0.7483 (mtp) REVERT: A 1282 ASP cc_start: 0.7705 (t70) cc_final: 0.7492 (t70) REVERT: A 1441 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 44 LEU cc_start: 0.8065 (mp) cc_final: 0.7846 (mt) REVERT: B 52 GLN cc_start: 0.8093 (mt0) cc_final: 0.7832 (mt0) REVERT: B 130 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8514 (ttpt) REVERT: B 223 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (m) REVERT: B 255 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7587 (mmm-85) REVERT: B 301 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7875 (p) REVERT: B 320 PHE cc_start: 0.8504 (t80) cc_final: 0.8164 (t80) REVERT: B 323 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 324 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6072 (mtm-85) REVERT: B 442 ASP cc_start: 0.7610 (m-30) cc_final: 0.7265 (m-30) REVERT: B 606 ASP cc_start: 0.8131 (t0) cc_final: 0.7852 (t0) REVERT: B 649 ASN cc_start: 0.8066 (t0) cc_final: 0.7717 (t0) REVERT: B 691 SER cc_start: 0.8672 (m) cc_final: 0.8384 (t) REVERT: B 812 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8190 (ttm-80) REVERT: B 826 GLU cc_start: 0.7584 (pt0) cc_final: 0.7297 (pt0) REVERT: B 896 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (mp) REVERT: B 1026 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 1171 MET cc_start: 0.8962 (mtm) cc_final: 0.8709 (mtp) REVERT: B 1172 MET cc_start: 0.8952 (mmm) cc_final: 0.8396 (mmt) REVERT: C 86 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8396 (ptt90) REVERT: C 258 ASP cc_start: 0.8262 (m-30) cc_final: 0.8050 (m-30) REVERT: C 260 GLN cc_start: 0.8210 (tt0) cc_final: 0.7811 (tt0) outliers start: 118 outliers final: 69 residues processed: 854 average time/residue: 1.7293 time to fit residues: 1713.0434 Evaluate side-chains 852 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 769 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL 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 116 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 163 optimal weight: 0.7980 chunk 329 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 36 ASN K 84 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 700 GLN A 757 GLN A 809 HIS A 982 ASN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 410 ASN B 582 GLN B 930 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN C 18 ASN C 32 ASN C 232 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107267 restraints weight = 43793.368| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.83 r_work: 0.3282 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32854 Z= 0.172 Angle : 0.620 13.628 44580 Z= 0.312 Chirality : 0.045 0.237 4982 Planarity : 0.004 0.062 5619 Dihedral : 12.587 145.239 4871 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.63 % Rotamer: Outliers : 3.28 % Allowed : 22.06 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3870 helix: 1.40 (0.14), residues: 1342 sheet: -0.04 (0.21), residues: 566 loop : -0.67 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.009 0.001 HIS A 204 PHE 0.024 0.002 PHE A 112 TYR 0.017 0.001 TYR A 413 ARG 0.012 0.001 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1384) hydrogen bonds : angle 4.87144 ( 3852) metal coordination : bond 0.00761 ( 32) metal coordination : angle 4.68392 ( 45) covalent geometry : bond 0.00406 (32822) covalent geometry : angle 0.60229 (44535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 790 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.4068 (OUTLIER) cc_final: 0.3730 (tt) REVERT: E 5 GLU cc_start: 0.7167 (tp30) cc_final: 0.6939 (tp30) REVERT: E 100 THR cc_start: 0.8315 (p) cc_final: 0.8012 (t) REVERT: E 162 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8554 (tpt90) REVERT: G 12 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8538 (mm) REVERT: G 77 PHE cc_start: 0.2712 (OUTLIER) cc_final: 0.2092 (t80) REVERT: G 145 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6695 (tt) REVERT: H 142 TYR cc_start: 0.8911 (m-80) cc_final: 0.8421 (m-80) REVERT: I 56 ASN cc_start: 0.8500 (t0) cc_final: 0.7860 (p0) REVERT: I 80 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8206 (mtt-85) REVERT: J 24 LEU cc_start: 0.8459 (mt) cc_final: 0.8158 (mp) REVERT: J 48 MET cc_start: 0.8902 (mmm) cc_final: 0.8683 (mmm) REVERT: K 29 ASN cc_start: 0.8601 (m-40) cc_final: 0.8377 (m-40) REVERT: L 26 ASN cc_start: 0.8194 (p0) cc_final: 0.7892 (p0) REVERT: L 44 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: A 116 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7781 (mtpp) REVERT: A 151 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7739 (mtmm) REVERT: A 154 CYS cc_start: 0.7022 (t) cc_final: 0.6761 (t) REVERT: A 201 GLU cc_start: 0.7751 (tp30) cc_final: 0.7434 (mm-30) REVERT: A 266 MET cc_start: 0.3596 (mmm) cc_final: 0.3297 (mmm) REVERT: A 289 GLN cc_start: 0.8275 (tt0) cc_final: 0.8054 (tt0) REVERT: A 290 LEU cc_start: 0.8738 (tp) cc_final: 0.8500 (tp) REVERT: A 321 GLU cc_start: 0.7590 (tt0) cc_final: 0.7257 (tt0) REVERT: A 382 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7762 (ttp-110) REVERT: A 401 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8270 (ttm170) REVERT: A 418 TYR cc_start: 0.8621 (m-80) cc_final: 0.8419 (m-80) REVERT: A 728 THR cc_start: 0.8495 (m) cc_final: 0.8100 (p) REVERT: A 783 GLN cc_start: 0.8526 (mt0) cc_final: 0.8312 (mt0) REVERT: A 845 GLU cc_start: 0.7972 (tt0) cc_final: 0.7702 (tt0) REVERT: A 849 ASP cc_start: 0.7532 (m-30) cc_final: 0.7266 (m-30) REVERT: A 927 GLU cc_start: 0.7372 (tp30) cc_final: 0.7130 (tp30) REVERT: A 964 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8037 (mp0) REVERT: A 1008 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8377 (tttm) REVERT: A 1034 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.6990 (tp40) REVERT: A 1042 ASN cc_start: 0.8533 (m-40) cc_final: 0.8277 (m-40) REVERT: A 1195 VAL cc_start: 0.7859 (t) cc_final: 0.7629 (m) REVERT: A 1196 TYR cc_start: 0.7264 (m-80) cc_final: 0.6360 (m-80) REVERT: A 1254 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7902 (ttpp) REVERT: A 1282 ASP cc_start: 0.7787 (t70) cc_final: 0.7586 (t70) REVERT: A 1428 MET cc_start: 0.8045 (tmm) cc_final: 0.7750 (tmm) REVERT: B 52 GLN cc_start: 0.8138 (mt0) cc_final: 0.7876 (mt0) REVERT: B 88 PHE cc_start: 0.7800 (m-80) cc_final: 0.7450 (m-80) REVERT: B 130 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8554 (ttpt) REVERT: B 223 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8289 (m) REVERT: B 255 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7626 (mmm-85) REVERT: B 301 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8014 (p) REVERT: B 323 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 442 ASP cc_start: 0.7707 (m-30) cc_final: 0.7352 (m-30) REVERT: B 456 GLN cc_start: 0.7518 (tt0) cc_final: 0.6789 (mt0) REVERT: B 606 ASP cc_start: 0.8208 (t0) cc_final: 0.7932 (t0) REVERT: B 649 ASN cc_start: 0.8235 (t0) cc_final: 0.7867 (t0) REVERT: B 666 ASP cc_start: 0.8233 (p0) cc_final: 0.8023 (p0) REVERT: B 691 SER cc_start: 0.8713 (m) cc_final: 0.8427 (t) REVERT: B 744 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7557 (mmm) REVERT: B 812 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8229 (ttm-80) REVERT: B 826 GLU cc_start: 0.7637 (pt0) cc_final: 0.7349 (pt0) REVERT: B 896 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 1026 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 1121 LEU cc_start: 0.8292 (mm) cc_final: 0.8030 (mp) REVERT: B 1171 MET cc_start: 0.8986 (mtm) cc_final: 0.8736 (mtp) REVERT: C 86 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8435 (ptt90) REVERT: C 260 GLN cc_start: 0.8281 (tt0) cc_final: 0.7881 (tt0) outliers start: 113 outliers final: 75 residues processed: 853 average time/residue: 1.6532 time to fit residues: 1630.9490 Evaluate side-chains 866 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 777 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL 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 116 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 58 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 322 optimal weight: 0.5980 chunk 365 optimal weight: 0.9990 chunk 343 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 36 ASN K 84 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 700 GLN A 757 GLN A 982 ASN A1244 ASN B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104905 restraints weight = 43909.229| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.62 r_work: 0.3295 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32854 Z= 0.175 Angle : 0.627 13.253 44580 Z= 0.316 Chirality : 0.046 0.242 4982 Planarity : 0.004 0.068 5619 Dihedral : 12.530 145.496 4867 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.06 % Favored : 94.68 % Rotamer: Outliers : 2.82 % Allowed : 22.99 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3870 helix: 1.36 (0.14), residues: 1342 sheet: -0.09 (0.21), residues: 566 loop : -0.70 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.006 0.001 HIS K 69 PHE 0.024 0.002 PHE B 320 TYR 0.019 0.002 TYR B1153 ARG 0.011 0.001 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1384) hydrogen bonds : angle 4.89730 ( 3852) metal coordination : bond 0.00762 ( 32) metal coordination : angle 4.52606 ( 45) covalent geometry : bond 0.00415 (32822) covalent geometry : angle 0.61108 (44535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 776 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.3984 (OUTLIER) cc_final: 0.3629 (tt) REVERT: E 5 GLU cc_start: 0.7178 (tp30) cc_final: 0.6779 (tp30) REVERT: E 100 THR cc_start: 0.8257 (p) cc_final: 0.7950 (t) REVERT: E 162 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8575 (tpt170) REVERT: F 109 TYR cc_start: 0.8562 (m-80) cc_final: 0.8280 (m-80) REVERT: G 12 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (mm) REVERT: G 77 PHE cc_start: 0.2690 (OUTLIER) cc_final: 0.2021 (t80) REVERT: H 142 TYR cc_start: 0.8894 (m-80) cc_final: 0.8407 (m-80) REVERT: I 56 ASN cc_start: 0.8470 (t0) cc_final: 0.7852 (p0) REVERT: I 80 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.8198 (mtt-85) REVERT: K 29 ASN cc_start: 0.8579 (m-40) cc_final: 0.8345 (m-40) REVERT: L 26 ASN cc_start: 0.8218 (p0) cc_final: 0.7935 (p0) REVERT: L 44 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: A 151 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7731 (mtmm) REVERT: A 154 CYS cc_start: 0.7000 (t) cc_final: 0.6737 (t) REVERT: A 201 GLU cc_start: 0.7731 (tp30) cc_final: 0.7419 (mm-30) REVERT: A 231 GLU cc_start: 0.7772 (mp0) cc_final: 0.7470 (mp0) REVERT: A 266 MET cc_start: 0.3602 (mmm) cc_final: 0.3280 (mmm) REVERT: A 289 GLN cc_start: 0.8251 (tt0) cc_final: 0.8003 (tt0) REVERT: A 290 LEU cc_start: 0.8732 (tp) cc_final: 0.8474 (tp) REVERT: A 321 GLU cc_start: 0.7572 (tt0) cc_final: 0.7250 (tt0) REVERT: A 382 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7743 (ttp-110) REVERT: A 401 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8238 (ttm170) REVERT: A 418 TYR cc_start: 0.8604 (m-80) cc_final: 0.8399 (m-80) REVERT: A 612 ASP cc_start: 0.7657 (m-30) cc_final: 0.7354 (p0) REVERT: A 728 THR cc_start: 0.8500 (m) cc_final: 0.8119 (p) REVERT: A 734 ARG cc_start: 0.8055 (mpp-170) cc_final: 0.7379 (ttm-80) REVERT: A 783 GLN cc_start: 0.8507 (mt0) cc_final: 0.8290 (mt0) REVERT: A 845 GLU cc_start: 0.7932 (tt0) cc_final: 0.7662 (tt0) REVERT: A 849 ASP cc_start: 0.7474 (m-30) cc_final: 0.7208 (m-30) REVERT: A 927 GLU cc_start: 0.7304 (tp30) cc_final: 0.7072 (tp30) REVERT: A 964 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8006 (mp0) REVERT: A 1008 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8365 (tttm) REVERT: A 1034 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.6959 (tp40) REVERT: A 1042 ASN cc_start: 0.8514 (m-40) cc_final: 0.8278 (m-40) REVERT: A 1195 VAL cc_start: 0.7859 (t) cc_final: 0.7642 (m) REVERT: A 1196 TYR cc_start: 0.7214 (m-80) cc_final: 0.6316 (m-80) REVERT: A 1246 ILE cc_start: 0.8784 (mt) cc_final: 0.8417 (mm) REVERT: A 1254 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7879 (ttpp) REVERT: A 1282 ASP cc_start: 0.7787 (t70) cc_final: 0.7582 (t70) REVERT: A 1415 THR cc_start: 0.8879 (p) cc_final: 0.8652 (p) REVERT: A 1428 MET cc_start: 0.8017 (tmm) cc_final: 0.7718 (tmm) REVERT: A 1441 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 88 PHE cc_start: 0.7829 (m-80) cc_final: 0.7508 (m-80) REVERT: B 223 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (m) REVERT: B 255 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: B 301 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (p) REVERT: B 323 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8553 (p) REVERT: B 442 ASP cc_start: 0.7675 (m-30) cc_final: 0.7322 (m-30) REVERT: B 456 GLN cc_start: 0.7488 (tt0) cc_final: 0.6774 (mt0) REVERT: B 606 ASP cc_start: 0.8155 (t0) cc_final: 0.7899 (t0) REVERT: B 649 ASN cc_start: 0.8250 (t0) cc_final: 0.7850 (t0) REVERT: B 666 ASP cc_start: 0.8252 (p0) cc_final: 0.8009 (p0) REVERT: B 691 SER cc_start: 0.8688 (m) cc_final: 0.8407 (t) REVERT: B 744 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7554 (mmm) REVERT: B 812 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8222 (ttm-80) REVERT: B 826 GLU cc_start: 0.7620 (pt0) cc_final: 0.7372 (pt0) REVERT: B 896 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 1026 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 1121 LEU cc_start: 0.8268 (mm) cc_final: 0.8048 (mp) REVERT: B 1171 MET cc_start: 0.8975 (mtm) cc_final: 0.8705 (mtp) REVERT: C 86 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8419 (ptt90) REVERT: C 258 ASP cc_start: 0.8261 (m-30) cc_final: 0.8050 (m-30) REVERT: C 260 GLN cc_start: 0.8284 (tt0) cc_final: 0.7851 (tt0) outliers start: 97 outliers final: 77 residues processed: 831 average time/residue: 1.7137 time to fit residues: 1655.3270 Evaluate side-chains 855 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 766 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL 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 153 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 252 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 206 optimal weight: 0.0470 chunk 139 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 194 optimal weight: 0.0570 chunk 110 optimal weight: 0.3980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 84 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 757 GLN A 861 GLN A 982 ASN A1410 HIS B 90 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108928 restraints weight = 43813.663| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.63 r_work: 0.3323 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32854 Z= 0.128 Angle : 0.603 13.510 44580 Z= 0.305 Chirality : 0.044 0.240 4982 Planarity : 0.004 0.062 5619 Dihedral : 12.414 145.627 4867 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.14 % Favored : 94.60 % Rotamer: Outliers : 2.59 % Allowed : 23.39 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3870 helix: 1.38 (0.14), residues: 1352 sheet: -0.00 (0.22), residues: 556 loop : -0.67 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS B 939 PHE 0.018 0.001 PHE A1284 TYR 0.020 0.001 TYR B1153 ARG 0.009 0.001 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 1384) hydrogen bonds : angle 4.84178 ( 3852) metal coordination : bond 0.00509 ( 32) metal coordination : angle 4.26362 ( 45) covalent geometry : bond 0.00297 (32822) covalent geometry : angle 0.58807 (44535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35446.55 seconds wall clock time: 608 minutes 12.36 seconds (36492.36 seconds total)