Starting phenix.real_space_refine on Sun Aug 9 06:55:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w8r_65749/08_2026/9w8r_65749.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 39 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20354 2.51 5 N 5657 2.21 5 O 6238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32477 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 203 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 9} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 390 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9378 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 647 SG CYS C 86 67.499 77.943 129.215 1.00142.84 S ATOM 664 SG CYS C 88 66.237 80.211 126.342 1.00152.01 S ATOM 697 SG CYS C 92 66.935 81.629 129.821 1.00123.18 S ATOM 720 SG CYS C 95 69.736 80.342 127.417 1.00114.32 S ATOM 5935 SG CYS I 7 126.928 116.090 27.523 1.00130.38 S ATOM 5960 SG CYS I 10 123.051 116.339 27.986 1.00127.84 S ATOM 6126 SG CYS I 29 124.534 113.281 26.341 1.00145.89 S ATOM 6150 SG CYS I 32 124.747 116.542 24.560 1.00128.82 S ATOM 6477 SG CYS I 75 147.433 105.753 65.941 1.00101.51 S ATOM 6499 SG CYS I 78 148.494 109.622 65.967 1.00105.21 S ATOM 6715 SG CYS I 103 145.088 108.223 67.472 1.00 97.58 S ATOM 6735 SG CYS I 106 145.955 108.664 63.868 1.00105.99 S ATOM 6880 SG CYS J 7 98.082 87.221 116.443 1.00 72.54 S ATOM 6903 SG CYS J 10 98.412 85.052 119.589 1.00 65.65 S ATOM 7183 SG CYS J 45 101.398 85.382 117.180 1.00 77.63 S ATOM 7189 SG CYS J 46 100.149 88.128 119.580 1.00 72.39 S ATOM 8369 SG CYS L 31 69.667 115.971 100.204 1.00 86.09 S ATOM 8389 SG CYS L 34 70.514 119.144 102.307 1.00 84.27 S ATOM 8493 SG CYS L 48 66.848 118.173 101.142 1.00 81.65 S ATOM 8516 SG CYS L 51 69.656 119.669 98.988 1.00100.09 S ATOM 10305 SG CYS A 107 75.038 73.708 21.584 1.00122.49 S ATOM 10329 SG CYS A 110 72.867 70.644 20.975 1.00134.05 S ATOM 10634 SG CYS A 148 76.173 70.871 19.184 1.00148.86 S ATOM 10772 SG CYS A 167 73.374 73.239 18.242 1.00134.26 S ATOM 10000 SG CYS A 67 50.559 74.000 62.287 1.00 97.69 S ATOM 10022 SG CYS A 70 50.899 70.432 63.667 1.00101.27 S ATOM 10075 SG CYS A 77 53.960 72.778 63.609 1.00 97.52 S ATOM 29522 SG CYS B1163 57.146 60.518 52.774 1.00 93.52 S ATOM 29540 SG CYS B1166 58.894 63.133 50.994 1.00 87.35 S ATOM 29665 SG CYS B1182 55.134 63.609 52.313 1.00 93.04 S ATOM 29684 SG CYS B1185 56.050 61.801 49.144 1.00101.92 S Time building chain proxies: 6.27, per 1000 atoms: 0.19 Number of scatterers: 32477 At special positions: 0 Unit cell: (161.82, 152.52, 155.31, 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 180 16.00 P 39 15.00 Mg 1 11.99 O 6238 8.00 N 5657 7.00 C 20354 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: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 51 sheets defined 38.6% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.947A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.795A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.610A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.509A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.573A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.536A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.978A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.029A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.885A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.511A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.762A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.730A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.810A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.209A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.813A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.601A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.609A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.732A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1269 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.888A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.504A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.024A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.527A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.657A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.612A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.656A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.439A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.539A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.521A pdb=" N LEU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.514A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.895A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.526A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.534A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 4.014A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.593A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.736A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.734A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.138A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.870A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.872A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.420A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.500A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AA9, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.708A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AB2, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.847A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AB4, first strand: chain 'I' and resid 14 through 17 removed outlier: 3.757A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 44 through 47 removed outlier: 3.725A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'L' and resid 37 through 40 removed outlier: 4.028A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 37 through 40 removed outlier: 4.028A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AC2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.888A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.716A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.609A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.597A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.076A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.635A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AD1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.271A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.862A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AD4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AD5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AD6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AD7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.644A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.179A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.179A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AE2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AE3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.186A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.045A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AE6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AE7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.408A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AE9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.611A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AF2, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AF3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AF4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AF5, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AF6, first strand: chain 'D' and resid 36 through 38 1412 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10727 1.34 - 1.46: 6237 1.46 - 1.58: 15807 1.58 - 1.70: 75 1.70 - 1.82: 288 Bond restraints: 33134 Sorted by residual: bond pdb=" P DG N 1 " pdb=" O5' DG N 1 " ideal model delta sigma weight residual 1.593 1.619 -0.026 1.00e-02 1.00e+04 6.88e+00 bond pdb=" P DG N 9 " pdb=" O5' DG N 9 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.74e+00 bond pdb=" P DA N 8 " pdb=" O5' DA N 8 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 4.00e+00 bond pdb=" P G P 9 " pdb=" O5' G P 9 " ideal model delta sigma weight residual 1.593 1.612 -0.019 1.00e-02 1.00e+04 3.55e+00 bond pdb=" C1' G P 9 " pdb=" N9 G P 9 " ideal model delta sigma weight residual 1.483 1.455 0.028 1.50e-02 4.44e+03 3.38e+00 ... (remaining 33129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 44493 2.28 - 4.56: 380 4.56 - 6.85: 28 6.85 - 9.13: 2 9.13 - 11.41: 1 Bond angle restraints: 44904 Sorted by residual: angle pdb=" C3' G P 7 " pdb=" C2' G P 7 " pdb=" C1' G P 7 " ideal model delta sigma weight residual 101.30 104.20 -2.90 7.00e-01 2.04e+00 1.72e+01 angle pdb=" C3' A P 15 " pdb=" C2' A P 15 " pdb=" C1' A P 15 " ideal model delta sigma weight residual 101.30 103.59 -2.29 7.00e-01 2.04e+00 1.07e+01 angle pdb=" C3' DG N 9 " pdb=" O3' DG N 9 " pdb=" P DG N 10 " ideal model delta sigma weight residual 119.70 123.46 -3.76 1.20e+00 6.94e-01 9.80e+00 angle pdb=" C3' DC T 12 " pdb=" C2' DC T 12 " pdb=" C1' DC T 12 " ideal model delta sigma weight residual 102.50 106.25 -3.75 1.20e+00 6.94e-01 9.78e+00 angle pdb=" O4' DG N 5 " pdb=" C4' DG N 5 " pdb=" C3' DG N 5 " ideal model delta sigma weight residual 106.00 107.85 -1.85 6.00e-01 2.78e+00 9.55e+00 ... (remaining 44899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.48: 19591 29.48 - 58.96: 564 58.96 - 88.45: 60 88.45 - 117.93: 2 117.93 - 147.41: 1 Dihedral angle restraints: 20218 sinusoidal: 8658 harmonic: 11560 Sorted by residual: dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DC T 16 " pdb=" C3' DC T 16 " pdb=" O3' DC T 16 " pdb=" P DT T 17 " ideal model delta sinusoidal sigma weight residual 220.00 72.59 147.41 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA PRO I 76 " pdb=" C PRO I 76 " pdb=" N LYS I 77 " pdb=" CA LYS I 77 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 20215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5002 0.122 - 0.244: 39 0.244 - 0.366: 0 0.366 - 0.488: 1 0.488 - 0.610: 9 Chirality restraints: 5051 Sorted by residual: chirality pdb=" P DG N 1 " pdb=" OP1 DG N 1 " pdb=" OP2 DG N 1 " pdb=" O5' DG N 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" P G P 7 " pdb=" OP1 G P 7 " pdb=" OP2 G P 7 " pdb=" O5' G P 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.19e+00 chirality pdb=" P DA N 8 " pdb=" OP1 DA N 8 " pdb=" OP2 DA N 8 " pdb=" O5' DA N 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 5048 not shown) Planarity restraints: 5690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A 245 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 14 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO G 15 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 15 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 15 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 8 " -0.002 2.00e-02 2.50e+03 1.10e-02 3.31e+00 pdb=" N9 DA N 8 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA N 8 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA N 8 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA N 8 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA N 8 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA N 8 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA N 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA N 8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA N 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA N 8 " -0.022 2.00e-02 2.50e+03 ... (remaining 5687 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 24 2.28 - 2.93: 13679 2.93 - 3.59: 49489 3.59 - 4.24: 81118 4.24 - 4.90: 135158 Nonbonded interactions: 279468 Sorted by model distance: nonbonded pdb=" O3' A P 15 " pdb="MG MG P 101 " model vdw 1.624 2.170 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.120 3.120 nonbonded pdb=" OG1 THR B 487 " pdb=" O ALA B 777 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A1115 " pdb=" OD1 ASN A1330 " model vdw 2.156 3.040 nonbonded pdb=" O ARG J 48 " pdb=" OG1 THR J 52 " model vdw 2.169 3.040 ... (remaining 279463 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: 2.950 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 34.650 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- 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 : 0.003 0.093 33166 Z= 0.152 Angle : 0.554 14.398 44949 Z= 0.300 Chirality : 0.049 0.610 5051 Planarity : 0.003 0.070 5690 Dihedral : 13.706 147.412 12732 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3936 helix: 1.27 (0.14), residues: 1356 sheet: -0.10 (0.21), residues: 616 loop : 0.30 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 47 TYR 0.019 0.001 TYR B 797 PHE 0.026 0.001 PHE A 444 TRP 0.011 0.001 TRP C 170 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (33134) covalent geometry : angle 0.52962 / 0.30 (44904) hydrogen bonds : bond 0.16828 / 11.02 ( 1383) hydrogen bonds : angle 6.56015 / 4.60 ( 3867) metal coordination : bond 0.00497 / 0.30 ( 32) metal coordination : angle 5.20984 / 3.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 GLU cc_start: 0.7308 (tt0) cc_final: 0.7054 (tp30) REVERT: E 7 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8261 (ptp-170) REVERT: E 83 CYS cc_start: 0.7290 (t) cc_final: 0.7038 (t) REVERT: E 90 VAL cc_start: 0.9271 (t) cc_final: 0.9070 (p) REVERT: E 94 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8808 (tppt) REVERT: E 102 GLU cc_start: 0.8862 (pp20) cc_final: 0.8643 (pp20) REVERT: E 124 VAL cc_start: 0.8596 (t) cc_final: 0.8338 (t) REVERT: F 72 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6637 (mmtt) REVERT: G 115 MET cc_start: 0.3776 (mpp) cc_final: 0.2653 (mpp) REVERT: I 11 ASN cc_start: 0.8581 (t0) cc_final: 0.7951 (t0) REVERT: J 23 ASN cc_start: 0.8292 (t0) cc_final: 0.8075 (m-40) REVERT: J 26 GLN cc_start: 0.8417 (tp-100) cc_final: 0.7934 (mp10) REVERT: K 5 ASP cc_start: 0.8677 (m-30) cc_final: 0.8460 (m-30) REVERT: K 106 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7254 (mm-30) REVERT: L 27 LEU cc_start: 0.8273 (mt) cc_final: 0.7633 (mp) REVERT: A 45 GLN cc_start: 0.8669 (mm110) cc_final: 0.8172 (mp10) REVERT: A 122 MET cc_start: 0.7675 (mmp) cc_final: 0.7384 (mmm) REVERT: A 281 HIS cc_start: 0.8228 (t-90) cc_final: 0.7678 (t-90) REVERT: A 693 VAL cc_start: 0.8598 (t) cc_final: 0.8373 (p) REVERT: A 1124 HIS cc_start: 0.8159 (m-70) cc_final: 0.7865 (m-70) REVERT: A 1207 LEU cc_start: 0.8444 (mm) cc_final: 0.7957 (mt) REVERT: B 90 ILE cc_start: 0.8677 (mt) cc_final: 0.8268 (pp) REVERT: B 296 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7784 (mm-30) REVERT: B 350 GLN cc_start: 0.8357 (tp40) cc_final: 0.8126 (tm-30) REVERT: B 358 LYS cc_start: 0.8684 (mttt) cc_final: 0.8358 (mmtp) REVERT: B 432 MET cc_start: 0.7587 (ttp) cc_final: 0.7243 (ptm) REVERT: B 434 ARG cc_start: 0.7812 (tmm160) cc_final: 0.7586 (ttp80) REVERT: B 620 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: B 662 MET cc_start: 0.8604 (mmp) cc_final: 0.8373 (mmm) REVERT: B 789 MET cc_start: 0.9254 (mmm) cc_final: 0.8875 (mmt) REVERT: D 12 ARG cc_start: 0.2953 (mmp80) cc_final: 0.1853 (ppt170) REVERT: H 31 THR cc_start: 0.8504 (t) cc_final: 0.8285 (p) REVERT: H 128 ASN cc_start: 0.7433 (p0) cc_final: 0.7143 (p0) outliers start: 0 outliers final: 1 residues processed: 663 average time/residue: 0.7810 time to fit residues: 599.7222 Evaluate side-chains 349 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1176 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 3 GLN E 5 ASN F 78 GLN I 90 GLN K 2 ASN K 104 ASN A 92 HIS A 171 GLN A 397 ASN A 587 HIS A 969 GLN A 975 HIS B 395 GLN B 513 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B 932 HIS B1104 HIS B1176 ASN B1177 HIS D 143 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069324 restraints weight = 57883.466| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.49 r_work: 0.2889 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33166 Z= 0.181 Angle : 0.646 15.013 44949 Z= 0.332 Chirality : 0.045 0.229 5051 Planarity : 0.005 0.081 5690 Dihedral : 8.878 139.958 4768 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.00 % Allowed : 10.05 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3936 helix: 1.14 (0.14), residues: 1382 sheet: -0.25 (0.20), residues: 620 loop : 0.24 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1274 TYR 0.022 0.002 TYR B1092 PHE 0.026 0.002 PHE A 219 TRP 0.010 0.001 TRP A 556 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (33134) covalent geometry : angle 0.62426 / 0.33 (44904) hydrogen bonds : bond 0.04023 / 2.72 ( 1383) hydrogen bonds : angle 5.19128 / 3.65 ( 3867) metal coordination : bond 0.00729 / 0.46 ( 32) metal coordination : angle 5.22954 / 3.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 390 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7533 (t0) REVERT: C 50 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7547 (mp0) REVERT: E 3 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7737 (tm130) REVERT: E 48 ASP cc_start: 0.8425 (p0) cc_final: 0.8193 (p0) REVERT: E 83 CYS cc_start: 0.7889 (t) cc_final: 0.7360 (t) REVERT: E 94 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8802 (tppp) REVERT: E 102 GLU cc_start: 0.8877 (pp20) cc_final: 0.8607 (pp20) REVERT: E 112 TYR cc_start: 0.8150 (p90) cc_final: 0.7794 (p90) REVERT: E 124 VAL cc_start: 0.8449 (t) cc_final: 0.8156 (t) REVERT: E 215 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6722 (mmt) REVERT: F 72 LYS cc_start: 0.6979 (mmtp) cc_final: 0.6504 (mmtt) REVERT: F 110 ASP cc_start: 0.8203 (p0) cc_final: 0.7962 (p0) REVERT: G 1 MET cc_start: 0.7866 (ttt) cc_final: 0.7200 (ptm) REVERT: G 50 ASP cc_start: 0.7176 (t0) cc_final: 0.6629 (t0) REVERT: G 57 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: G 65 ASP cc_start: 0.7959 (t0) cc_final: 0.7636 (t0) REVERT: G 109 PHE cc_start: 0.6587 (t80) cc_final: 0.6361 (t80) REVERT: G 115 MET cc_start: 0.3587 (mpp) cc_final: 0.3369 (mpp) REVERT: I 11 ASN cc_start: 0.8496 (t0) cc_final: 0.8116 (t0) REVERT: I 13 MET cc_start: 0.8383 (ptm) cc_final: 0.7938 (ttm) REVERT: I 27 PHE cc_start: 0.7942 (m-10) cc_final: 0.7502 (m-80) REVERT: I 28 GLU cc_start: 0.8205 (tt0) cc_final: 0.7780 (tp30) REVERT: I 47 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8297 (mm-30) REVERT: I 61 ASP cc_start: 0.8567 (p0) cc_final: 0.8132 (p0) REVERT: J 23 ASN cc_start: 0.8026 (t0) cc_final: 0.7725 (m-40) REVERT: J 26 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8118 (mp10) REVERT: J 29 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7970 (tm-30) REVERT: K 5 ASP cc_start: 0.8621 (m-30) cc_final: 0.8395 (m-30) REVERT: K 54 ARG cc_start: 0.8648 (tpp80) cc_final: 0.8373 (tpt170) REVERT: K 106 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7395 (mm-30) REVERT: A 45 GLN cc_start: 0.8648 (mm110) cc_final: 0.8234 (mp10) REVERT: A 74 MET cc_start: 0.8802 (mtm) cc_final: 0.8545 (mtm) REVERT: A 281 HIS cc_start: 0.8546 (t-90) cc_final: 0.8045 (t-90) REVERT: A 287 HIS cc_start: 0.8227 (t70) cc_final: 0.8014 (t70) REVERT: A 393 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7342 (mpt-90) REVERT: A 693 VAL cc_start: 0.8528 (t) cc_final: 0.8260 (p) REVERT: A 1218 GLN cc_start: 0.8874 (mt0) cc_final: 0.8611 (mt0) REVERT: A 1307 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 296 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7892 (tp30) REVERT: B 350 GLN cc_start: 0.8494 (tp40) cc_final: 0.7980 (tm-30) REVERT: B 354 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7790 (p0) REVERT: B 358 LYS cc_start: 0.8682 (mttt) cc_final: 0.8240 (mmmm) REVERT: B 432 MET cc_start: 0.7667 (ttp) cc_final: 0.7422 (ptm) REVERT: B 561 TRP cc_start: 0.8315 (m100) cc_final: 0.8049 (m100) REVERT: B 620 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.7725 (mmm-85) REVERT: D 14 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7053 (ptp-170) REVERT: H 31 THR cc_start: 0.8634 (t) cc_final: 0.8425 (p) outliers start: 70 outliers final: 20 residues processed: 428 average time/residue: 0.7434 time to fit residues: 374.0138 Evaluate side-chains 358 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 330 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 209 optimal weight: 4.9990 chunk 220 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 64 optimal weight: 50.0000 chunk 343 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 78 GLN A1258 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.069990 restraints weight = 57332.599| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.48 r_work: 0.2909 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33166 Z= 0.125 Angle : 0.565 13.314 44949 Z= 0.290 Chirality : 0.043 0.262 5051 Planarity : 0.004 0.069 5690 Dihedral : 8.780 139.089 4766 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 11.76 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3936 helix: 1.15 (0.14), residues: 1390 sheet: -0.23 (0.20), residues: 614 loop : 0.18 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 42 TYR 0.022 0.001 TYR G 167 PHE 0.025 0.001 PHE A 219 TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (33134) covalent geometry : angle 0.54619 / 0.29 (44904) hydrogen bonds : bond 0.03806 / 2.57 ( 1383) hydrogen bonds : angle 4.96238 / 3.48 ( 3867) metal coordination : bond 0.00436 / 0.29 ( 32) metal coordination : angle 4.65216 / 2.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 0.921 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: C 26 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7714 (t0) REVERT: C 50 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7573 (mp0) REVERT: E 3 GLN cc_start: 0.8601 (pm20) cc_final: 0.8066 (tm-30) REVERT: E 66 GLU cc_start: 0.8511 (mp0) cc_final: 0.8303 (pm20) REVERT: E 83 CYS cc_start: 0.7796 (t) cc_final: 0.7353 (t) REVERT: E 94 LYS cc_start: 0.9188 (ttpt) cc_final: 0.8916 (tppp) REVERT: E 102 GLU cc_start: 0.8832 (pp20) cc_final: 0.8589 (pp20) REVERT: E 112 TYR cc_start: 0.8275 (p90) cc_final: 0.7712 (p90) REVERT: E 124 VAL cc_start: 0.8470 (t) cc_final: 0.8169 (t) REVERT: E 215 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: F 72 LYS cc_start: 0.6909 (mmtp) cc_final: 0.6440 (mmtt) REVERT: F 110 ASP cc_start: 0.8404 (p0) cc_final: 0.8140 (p0) REVERT: G 57 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: G 65 ASP cc_start: 0.7903 (t0) cc_final: 0.7463 (t0) REVERT: G 69 GLU cc_start: 0.7539 (pt0) cc_final: 0.6896 (pp20) REVERT: G 109 PHE cc_start: 0.6566 (t80) cc_final: 0.6346 (t80) REVERT: G 115 MET cc_start: 0.4127 (mpp) cc_final: 0.3577 (mtm) REVERT: I 11 ASN cc_start: 0.8545 (t0) cc_final: 0.8132 (t0) REVERT: I 13 MET cc_start: 0.8402 (ptm) cc_final: 0.8011 (ttm) REVERT: I 27 PHE cc_start: 0.7964 (m-10) cc_final: 0.7292 (m-80) REVERT: I 28 GLU cc_start: 0.8267 (tt0) cc_final: 0.7971 (tp30) REVERT: I 61 ASP cc_start: 0.8621 (p0) cc_final: 0.8151 (p0) REVERT: I 87 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7955 (tp40) REVERT: J 23 ASN cc_start: 0.8011 (t0) cc_final: 0.7740 (m-40) REVERT: J 26 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8262 (mt0) REVERT: J 29 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7913 (tm-30) REVERT: K 5 ASP cc_start: 0.8716 (m-30) cc_final: 0.8510 (m-30) REVERT: K 54 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8341 (tpt170) REVERT: K 106 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7451 (mm-30) REVERT: A 45 GLN cc_start: 0.8639 (mm110) cc_final: 0.8238 (mp10) REVERT: A 74 MET cc_start: 0.8827 (mtm) cc_final: 0.8589 (mtm) REVERT: A 281 HIS cc_start: 0.8485 (t-90) cc_final: 0.7968 (t-90) REVERT: A 320 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8417 (ttm110) REVERT: A 393 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7322 (mpt-90) REVERT: A 693 VAL cc_start: 0.8637 (t) cc_final: 0.8379 (p) REVERT: A 915 SER cc_start: 0.8027 (m) cc_final: 0.7506 (p) REVERT: A 1191 TRP cc_start: 0.8248 (m100) cc_final: 0.7881 (m100) REVERT: A 1218 GLN cc_start: 0.8814 (mt0) cc_final: 0.8546 (mt0) REVERT: A 1285 MET cc_start: 0.7652 (mmm) cc_final: 0.7372 (mmp) REVERT: A 1307 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: A 1330 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7702 (p0) REVERT: B 255 GLN cc_start: 0.8201 (mt0) cc_final: 0.7935 (mt0) REVERT: B 296 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7948 (tp30) REVERT: B 350 GLN cc_start: 0.8486 (tp40) cc_final: 0.7970 (tm-30) REVERT: B 354 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7810 (p0) REVERT: B 358 LYS cc_start: 0.8690 (mttt) cc_final: 0.8257 (mmmm) REVERT: B 432 MET cc_start: 0.7571 (ttp) cc_final: 0.7370 (ptm) REVERT: B 434 ARG cc_start: 0.6978 (ttp80) cc_final: 0.6766 (ttp80) REVERT: B 561 TRP cc_start: 0.8344 (m100) cc_final: 0.8062 (m100) REVERT: B 620 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7763 (mmm-85) REVERT: B 1021 MET cc_start: 0.9399 (mtm) cc_final: 0.9182 (mtp) REVERT: D 14 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7069 (ptp-170) REVERT: D 39 ASN cc_start: 0.7201 (p0) cc_final: 0.6738 (p0) REVERT: D 214 LEU cc_start: 0.7991 (tm) cc_final: 0.7663 (mp) REVERT: H 123 MET cc_start: 0.8679 (ttp) cc_final: 0.8056 (ttp) outliers start: 65 outliers final: 26 residues processed: 396 average time/residue: 0.7144 time to fit residues: 332.3072 Evaluate side-chains 362 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 327 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 246 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 135 GLN E 3 GLN E 5 ASN F 78 GLN G 96 GLN K 2 ASN K 89 ASN A 935 GLN A1171 GLN B 306 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1177 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066592 restraints weight = 57287.086| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.45 r_work: 0.2833 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 33166 Z= 0.228 Angle : 0.640 16.094 44949 Z= 0.327 Chirality : 0.046 0.234 5051 Planarity : 0.005 0.106 5690 Dihedral : 8.865 140.847 4766 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 2.68 % Allowed : 12.44 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3936 helix: 0.99 (0.14), residues: 1385 sheet: -0.30 (0.20), residues: 618 loop : 0.14 (0.15), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1244 TYR 0.031 0.002 TYR B1092 PHE 0.029 0.002 PHE A 219 TRP 0.015 0.001 TRP B 31 HIS 0.007 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (33134) covalent geometry : angle 0.61570 / 0.33 (44904) hydrogen bonds : bond 0.04002 / 2.70 ( 1383) hydrogen bonds : angle 4.93242 / 3.47 ( 3867) metal coordination : bond 0.00839 / 0.53 ( 32) metal coordination : angle 5.53229 / 3.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 345 time to evaluate : 1.287 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: C 50 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7765 (mp0) REVERT: E 3 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7876 (tm130) REVERT: E 48 ASP cc_start: 0.8535 (p0) cc_final: 0.8002 (p0) REVERT: E 94 LYS cc_start: 0.9243 (ttpt) cc_final: 0.8946 (tppp) REVERT: E 102 GLU cc_start: 0.8822 (pp20) cc_final: 0.8564 (pp20) REVERT: E 215 MET cc_start: 0.7287 (mmp) cc_final: 0.7037 (mmt) REVERT: F 110 ASP cc_start: 0.8460 (p0) cc_final: 0.7930 (p0) REVERT: F 112 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7852 (mp0) REVERT: G 21 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.8045 (ppt170) REVERT: G 65 ASP cc_start: 0.8004 (t0) cc_final: 0.7495 (t0) REVERT: G 69 GLU cc_start: 0.7788 (pt0) cc_final: 0.7011 (pp20) REVERT: G 73 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7639 (mtpp) REVERT: G 109 PHE cc_start: 0.6532 (t80) cc_final: 0.6293 (t80) REVERT: G 115 MET cc_start: 0.3934 (mpp) cc_final: 0.3344 (mtm) REVERT: I 13 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: I 27 PHE cc_start: 0.7921 (m-10) cc_final: 0.7462 (m-80) REVERT: I 61 ASP cc_start: 0.8631 (p0) cc_final: 0.8187 (p0) REVERT: J 26 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8475 (mt0) REVERT: J 29 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7856 (tm-30) REVERT: K 5 ASP cc_start: 0.8881 (m-30) cc_final: 0.8636 (m-30) REVERT: K 11 LEU cc_start: 0.9152 (mt) cc_final: 0.8896 (mp) REVERT: K 54 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8445 (tpt90) REVERT: K 106 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7640 (mm-30) REVERT: A 45 GLN cc_start: 0.8732 (mm110) cc_final: 0.8271 (mp10) REVERT: A 74 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8510 (mtm) REVERT: A 281 HIS cc_start: 0.8528 (t-90) cc_final: 0.8039 (t-90) REVERT: A 320 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8355 (ttm110) REVERT: A 393 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7449 (mpt-90) REVERT: A 693 VAL cc_start: 0.8804 (t) cc_final: 0.8589 (p) REVERT: A 929 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 1133 LEU cc_start: 0.8664 (mt) cc_final: 0.8282 (tm) REVERT: A 1191 TRP cc_start: 0.8275 (m100) cc_final: 0.7772 (m100) REVERT: A 1218 GLN cc_start: 0.8857 (mt0) cc_final: 0.8541 (mt0) REVERT: A 1307 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 1330 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7968 (p0) REVERT: B 173 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8690 (ptp) REVERT: B 228 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: B 350 GLN cc_start: 0.8417 (tp40) cc_final: 0.7877 (tm-30) REVERT: B 354 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 358 LYS cc_start: 0.8635 (mttt) cc_final: 0.8230 (mmtp) REVERT: B 561 TRP cc_start: 0.8428 (m100) cc_final: 0.8192 (m100) REVERT: B 878 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7555 (mp10) REVERT: B 1021 MET cc_start: 0.9518 (mtm) cc_final: 0.9297 (mtp) REVERT: D 123 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6923 (mt) REVERT: H 123 MET cc_start: 0.8973 (ttp) cc_final: 0.8509 (ttp) REVERT: H 138 GLU cc_start: 0.8348 (pm20) cc_final: 0.8146 (pm20) outliers start: 94 outliers final: 35 residues processed: 403 average time/residue: 0.7545 time to fit residues: 356.6372 Evaluate side-chains 365 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 202 optimal weight: 0.4980 chunk 220 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 391 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 3 GLN F 78 GLN I 11 ASN I 89 GLN L 53 HIS A 479 ASN B 306 ASN B 592 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 HIS H 11 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066406 restraints weight = 57612.822| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.44 r_work: 0.2832 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 33166 Z= 0.210 Angle : 0.596 15.772 44949 Z= 0.304 Chirality : 0.045 0.240 5051 Planarity : 0.004 0.069 5690 Dihedral : 8.843 140.555 4766 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.03 % Allowed : 14.41 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3936 helix: 1.01 (0.14), residues: 1386 sheet: -0.34 (0.20), residues: 624 loop : 0.13 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 434 TYR 0.020 0.002 TYR G 51 PHE 0.027 0.002 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (33134) covalent geometry : angle 0.57160 / 0.30 (44904) hydrogen bonds : bond 0.03829 / 2.59 ( 1383) hydrogen bonds : angle 4.87307 / 3.44 ( 3867) metal coordination : bond 0.00777 / 0.51 ( 32) metal coordination : angle 5.33131 / 3.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 331 time to evaluate : 1.294 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: E 7 ARG cc_start: 0.8379 (ptm160) cc_final: 0.8044 (ptp-170) REVERT: E 102 GLU cc_start: 0.8809 (pp20) cc_final: 0.8565 (pp20) REVERT: E 112 TYR cc_start: 0.8325 (p90) cc_final: 0.7803 (p90) REVERT: E 124 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8300 (t) REVERT: E 215 MET cc_start: 0.7295 (mmp) cc_final: 0.7055 (mmt) REVERT: F 110 ASP cc_start: 0.8437 (p0) cc_final: 0.7927 (p0) REVERT: F 112 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7825 (mp0) REVERT: G 65 ASP cc_start: 0.8123 (t0) cc_final: 0.7589 (t0) REVERT: G 69 GLU cc_start: 0.7849 (pt0) cc_final: 0.6979 (pp20) REVERT: G 73 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7661 (mtpp) REVERT: G 109 PHE cc_start: 0.6532 (t80) cc_final: 0.6285 (t80) REVERT: G 115 MET cc_start: 0.3893 (mpp) cc_final: 0.3303 (mtt) REVERT: I 13 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7856 (ttm) REVERT: I 28 GLU cc_start: 0.8365 (tt0) cc_final: 0.8135 (tp30) REVERT: I 42 LEU cc_start: 0.9109 (mp) cc_final: 0.8862 (mm) REVERT: I 54 GLU cc_start: 0.6920 (pt0) cc_final: 0.6705 (pt0) REVERT: I 61 ASP cc_start: 0.8683 (p0) cc_final: 0.8321 (p0) REVERT: I 89 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8302 (mm110) REVERT: J 26 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8530 (mt0) REVERT: J 29 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7753 (tm-30) REVERT: K 54 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8440 (tpt170) REVERT: L 66 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8512 (tp40) REVERT: A 45 GLN cc_start: 0.8859 (mm110) cc_final: 0.8424 (mp10) REVERT: A 74 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (mtm) REVERT: A 133 LYS cc_start: 0.8977 (tppp) cc_final: 0.8770 (mtmm) REVERT: A 281 HIS cc_start: 0.8552 (t-90) cc_final: 0.8092 (t-90) REVERT: A 320 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8324 (ttm110) REVERT: A 393 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7456 (mpt-90) REVERT: A 915 SER cc_start: 0.8022 (m) cc_final: 0.7677 (p) REVERT: A 1133 LEU cc_start: 0.8664 (mt) cc_final: 0.8326 (tm) REVERT: A 1191 TRP cc_start: 0.8301 (m100) cc_final: 0.7773 (m100) REVERT: A 1218 GLN cc_start: 0.8801 (mt0) cc_final: 0.8566 (mt0) REVERT: A 1312 ASN cc_start: 0.8238 (t0) cc_final: 0.7328 (t0) REVERT: A 1330 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 173 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8699 (ptp) REVERT: B 228 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: B 350 GLN cc_start: 0.8439 (tp40) cc_final: 0.7960 (tm-30) REVERT: B 354 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7771 (p0) REVERT: B 358 LYS cc_start: 0.8656 (mttt) cc_final: 0.8197 (mmmm) REVERT: B 561 TRP cc_start: 0.8455 (m100) cc_final: 0.8230 (m100) REVERT: B 620 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.7791 (mmm-85) REVERT: B 878 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7557 (mp10) REVERT: B 1021 MET cc_start: 0.9526 (mtm) cc_final: 0.9205 (mtp) REVERT: D 123 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6926 (mt) REVERT: H 123 MET cc_start: 0.8975 (ttp) cc_final: 0.8665 (ttp) REVERT: H 138 GLU cc_start: 0.8263 (pm20) cc_final: 0.7796 (pm20) outliers start: 71 outliers final: 23 residues processed: 372 average time/residue: 0.7868 time to fit residues: 342.3957 Evaluate side-chains 348 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 274 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 31 optimal weight: 0.0030 chunk 92 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 385 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 18 optimal weight: 0.0040 chunk 346 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.067612 restraints weight = 57449.862| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.45 r_work: 0.2876 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33166 Z= 0.117 Angle : 0.551 13.280 44949 Z= 0.281 Chirality : 0.043 0.198 5051 Planarity : 0.004 0.069 5690 Dihedral : 8.758 138.800 4766 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.63 % Allowed : 15.21 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3936 helix: 1.13 (0.14), residues: 1387 sheet: -0.25 (0.20), residues: 617 loop : 0.17 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 434 TYR 0.019 0.001 TYR G 167 PHE 0.024 0.001 PHE A 219 TRP 0.011 0.001 TRP C 201 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33134) covalent geometry : angle 0.53068 / 0.28 (44904) hydrogen bonds : bond 0.03402 / 2.30 ( 1383) hydrogen bonds : angle 4.72576 / 3.33 ( 3867) metal coordination : bond 0.00420 / 0.28 ( 32) metal coordination : angle 4.66729 / 2.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 1.225 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: E 3 GLN cc_start: 0.8560 (pm20) cc_final: 0.8293 (pm20) REVERT: E 7 ARG cc_start: 0.8330 (ptm160) cc_final: 0.8079 (ptp-170) REVERT: E 94 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8906 (tppp) REVERT: E 102 GLU cc_start: 0.8775 (pp20) cc_final: 0.8514 (pp20) REVERT: E 112 TYR cc_start: 0.8217 (p90) cc_final: 0.7894 (p90) REVERT: E 215 MET cc_start: 0.7275 (mmp) cc_final: 0.7066 (mmt) REVERT: F 110 ASP cc_start: 0.8435 (p0) cc_final: 0.7880 (p0) REVERT: F 112 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7779 (mp0) REVERT: G 21 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7916 (ptm-80) REVERT: G 50 ASP cc_start: 0.8258 (m-30) cc_final: 0.7728 (t0) REVERT: G 65 ASP cc_start: 0.8071 (t0) cc_final: 0.7484 (t0) REVERT: G 69 GLU cc_start: 0.7870 (pt0) cc_final: 0.7042 (pp20) REVERT: G 109 PHE cc_start: 0.6613 (t80) cc_final: 0.6351 (t80) REVERT: G 115 MET cc_start: 0.3951 (mpp) cc_final: 0.3345 (mtt) REVERT: I 13 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7850 (ttt) REVERT: I 42 LEU cc_start: 0.9095 (mp) cc_final: 0.8834 (mm) REVERT: I 61 ASP cc_start: 0.8679 (p0) cc_final: 0.8340 (p0) REVERT: I 89 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8140 (mm110) REVERT: J 26 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8588 (mt0) REVERT: J 29 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7775 (tm-30) REVERT: K 54 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8468 (tpt170) REVERT: K 111 LEU cc_start: 0.8944 (tp) cc_final: 0.8654 (mm) REVERT: L 66 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8430 (tp40) REVERT: A 45 GLN cc_start: 0.8842 (mm110) cc_final: 0.8288 (mp10) REVERT: A 74 MET cc_start: 0.8663 (mtm) cc_final: 0.8364 (mtm) REVERT: A 133 LYS cc_start: 0.8989 (tppp) cc_final: 0.8779 (mtmm) REVERT: A 281 HIS cc_start: 0.8493 (t-90) cc_final: 0.7986 (t-90) REVERT: A 311 GLN cc_start: 0.8165 (mt0) cc_final: 0.7786 (tt0) REVERT: A 320 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8319 (ttm110) REVERT: A 393 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7507 (mpt-90) REVERT: A 915 SER cc_start: 0.7975 (m) cc_final: 0.7647 (p) REVERT: A 1133 LEU cc_start: 0.8683 (mt) cc_final: 0.8369 (tm) REVERT: A 1218 GLN cc_start: 0.8828 (mt0) cc_final: 0.8527 (mt0) REVERT: A 1330 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7950 (p0) REVERT: A 1336 MET cc_start: 0.8833 (ttp) cc_final: 0.8612 (ttp) REVERT: A 1446 ASP cc_start: 0.7775 (t0) cc_final: 0.7036 (t0) REVERT: B 101 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8972 (mtt) REVERT: B 173 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8621 (ptp) REVERT: B 228 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8035 (mtpp) REVERT: B 350 GLN cc_start: 0.8397 (tp40) cc_final: 0.7922 (tm-30) REVERT: B 358 LYS cc_start: 0.8668 (mttt) cc_final: 0.8205 (mmmm) REVERT: B 434 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6632 (ttp80) REVERT: B 561 TRP cc_start: 0.8448 (m100) cc_final: 0.8185 (m100) REVERT: B 620 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.7811 (mmm-85) REVERT: B 878 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7558 (mp10) REVERT: B 1021 MET cc_start: 0.9491 (mtm) cc_final: 0.9280 (mtp) REVERT: B 1138 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (mmm) REVERT: D 35 LEU cc_start: 0.7691 (pp) cc_final: 0.7382 (tm) REVERT: D 123 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6934 (mt) REVERT: H 123 MET cc_start: 0.8957 (ttp) cc_final: 0.8650 (ttp) REVERT: H 138 GLU cc_start: 0.8313 (pm20) cc_final: 0.7954 (pm20) outliers start: 57 outliers final: 24 residues processed: 374 average time/residue: 0.7869 time to fit residues: 343.1185 Evaluate side-chains 354 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 257 optimal weight: 0.0980 chunk 375 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN I 11 ASN B 531 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1013 ASN B1177 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067669 restraints weight = 57747.858| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.45 r_work: 0.2861 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33166 Z= 0.124 Angle : 0.547 12.502 44949 Z= 0.279 Chirality : 0.043 0.193 5051 Planarity : 0.004 0.070 5690 Dihedral : 8.729 138.696 4766 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.91 % Allowed : 15.15 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3936 helix: 1.20 (0.14), residues: 1386 sheet: -0.23 (0.20), residues: 611 loop : 0.19 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 67 TYR 0.019 0.001 TYR G 167 PHE 0.025 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.004 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (33134) covalent geometry : angle 0.52954 / 0.28 (44904) hydrogen bonds : bond 0.03370 / 2.28 ( 1383) hydrogen bonds : angle 4.65700 / 3.28 ( 3867) metal coordination : bond 0.00442 / 0.29 ( 32) metal coordination : angle 4.40975 / 2.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 1.271 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: C 155 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7676 (pp) REVERT: E 3 GLN cc_start: 0.8570 (pm20) cc_final: 0.8305 (pm20) REVERT: E 7 ARG cc_start: 0.8328 (ptm160) cc_final: 0.8069 (ptp-170) REVERT: E 94 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8906 (tppp) REVERT: E 102 GLU cc_start: 0.8782 (pp20) cc_final: 0.8511 (pp20) REVERT: E 215 MET cc_start: 0.7274 (mmp) cc_final: 0.7065 (mmt) REVERT: F 110 ASP cc_start: 0.8450 (p0) cc_final: 0.7913 (p0) REVERT: F 112 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7800 (mp0) REVERT: G 50 ASP cc_start: 0.8339 (m-30) cc_final: 0.7924 (t70) REVERT: G 65 ASP cc_start: 0.8239 (t0) cc_final: 0.7646 (t0) REVERT: G 69 GLU cc_start: 0.7831 (pt0) cc_final: 0.7019 (pp20) REVERT: G 73 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7652 (mtpp) REVERT: G 109 PHE cc_start: 0.6670 (t80) cc_final: 0.6433 (t80) REVERT: G 115 MET cc_start: 0.3895 (mpp) cc_final: 0.3239 (mtt) REVERT: I 13 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7819 (ttt) REVERT: I 61 ASP cc_start: 0.8720 (p0) cc_final: 0.8422 (p0) REVERT: I 89 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8047 (mm110) REVERT: J 26 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8562 (mt0) REVERT: J 29 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7840 (tm-30) REVERT: K 54 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8474 (tpt170) REVERT: K 111 LEU cc_start: 0.8905 (tp) cc_final: 0.8629 (mm) REVERT: L 66 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8272 (tp-100) REVERT: A 45 GLN cc_start: 0.8844 (mm110) cc_final: 0.8288 (mp10) REVERT: A 74 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: A 133 LYS cc_start: 0.8991 (tppp) cc_final: 0.8694 (mttm) REVERT: A 281 HIS cc_start: 0.8510 (t-90) cc_final: 0.8008 (t-90) REVERT: A 320 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8334 (ttm110) REVERT: A 393 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7533 (mpt-90) REVERT: A 915 SER cc_start: 0.7916 (m) cc_final: 0.7604 (p) REVERT: A 1133 LEU cc_start: 0.8673 (mt) cc_final: 0.8359 (tm) REVERT: A 1191 TRP cc_start: 0.8321 (m100) cc_final: 0.7753 (m100) REVERT: A 1218 GLN cc_start: 0.8836 (mt0) cc_final: 0.8540 (mt0) REVERT: A 1330 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7998 (p0) REVERT: A 1446 ASP cc_start: 0.7719 (t0) cc_final: 0.7017 (t0) REVERT: B 96 TYR cc_start: 0.8963 (m-80) cc_final: 0.8219 (m-80) REVERT: B 101 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: B 173 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8576 (ptp) REVERT: B 228 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8055 (mtpp) REVERT: B 313 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8595 (ttp) REVERT: B 350 GLN cc_start: 0.8400 (tp40) cc_final: 0.7904 (tm-30) REVERT: B 358 LYS cc_start: 0.8674 (mttt) cc_final: 0.8214 (mmmm) REVERT: B 561 TRP cc_start: 0.8452 (m100) cc_final: 0.8191 (m100) REVERT: B 620 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: B 878 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7553 (mp10) REVERT: B 948 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8468 (mp) REVERT: B 1021 MET cc_start: 0.9494 (mtm) cc_final: 0.9287 (mtp) REVERT: D 35 LEU cc_start: 0.7732 (pp) cc_final: 0.7422 (tm) REVERT: D 123 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6902 (mt) REVERT: D 214 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7578 (mp) REVERT: H 27 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7553 (mp0) REVERT: H 123 MET cc_start: 0.8973 (ttp) cc_final: 0.8673 (ttp) REVERT: H 138 GLU cc_start: 0.8304 (pm20) cc_final: 0.7936 (pm20) outliers start: 67 outliers final: 28 residues processed: 365 average time/residue: 0.8080 time to fit residues: 343.3163 Evaluate side-chains 357 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 299 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 393 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 313 optimal weight: 0.4980 chunk 298 optimal weight: 4.9990 chunk 382 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN B 531 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.066698 restraints weight = 57760.037| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.46 r_work: 0.2838 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33166 Z= 0.160 Angle : 0.571 13.551 44949 Z= 0.288 Chirality : 0.043 0.202 5051 Planarity : 0.004 0.070 5690 Dihedral : 8.752 139.418 4766 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.66 % Allowed : 15.72 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3936 helix: 1.20 (0.14), residues: 1385 sheet: -0.19 (0.21), residues: 612 loop : 0.17 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 434 TYR 0.019 0.001 TYR G 167 PHE 0.026 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (33134) covalent geometry : angle 0.55072 / 0.29 (44904) hydrogen bonds : bond 0.03490 / 2.37 ( 1383) hydrogen bonds : angle 4.68264 / 3.30 ( 3867) metal coordination : bond 0.00653 / 0.41 ( 32) metal coordination : angle 4.75582 / 2.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 1.199 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: C 155 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7727 (pp) REVERT: E 3 GLN cc_start: 0.8608 (pm20) cc_final: 0.8356 (pm20) REVERT: E 7 ARG cc_start: 0.8343 (ptm160) cc_final: 0.8068 (ptp-170) REVERT: E 52 ARG cc_start: 0.8744 (mmt180) cc_final: 0.8530 (mpt90) REVERT: E 94 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8904 (tppp) REVERT: E 102 GLU cc_start: 0.8767 (pp20) cc_final: 0.8475 (pp20) REVERT: E 121 MET cc_start: 0.8443 (mmt) cc_final: 0.8040 (mmm) REVERT: E 215 MET cc_start: 0.7275 (mmp) cc_final: 0.7056 (mmt) REVERT: F 110 ASP cc_start: 0.8454 (p0) cc_final: 0.7914 (p0) REVERT: F 112 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7784 (mp0) REVERT: F 114 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7520 (pt0) REVERT: G 65 ASP cc_start: 0.8279 (t0) cc_final: 0.7708 (t0) REVERT: G 69 GLU cc_start: 0.7773 (pt0) cc_final: 0.6913 (pp20) REVERT: G 73 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7712 (mtpp) REVERT: G 75 ARG cc_start: 0.7686 (mmt180) cc_final: 0.7170 (mmt180) REVERT: G 109 PHE cc_start: 0.6671 (t80) cc_final: 0.6439 (t80) REVERT: G 115 MET cc_start: 0.3869 (mpp) cc_final: 0.3216 (mtt) REVERT: I 13 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7871 (ttt) REVERT: I 22 ASN cc_start: 0.8607 (m-40) cc_final: 0.8281 (t0) REVERT: I 54 GLU cc_start: 0.6941 (pt0) cc_final: 0.6719 (pt0) REVERT: I 61 ASP cc_start: 0.8720 (p0) cc_final: 0.8440 (p0) REVERT: I 89 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8200 (mm110) REVERT: J 26 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8565 (mt0) REVERT: J 29 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7841 (tm-30) REVERT: K 54 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8468 (tpt170) REVERT: K 106 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7675 (mt-10) REVERT: L 66 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8359 (tp40) REVERT: A 45 GLN cc_start: 0.8876 (mm110) cc_final: 0.8376 (mp10) REVERT: A 74 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8357 (mtm) REVERT: A 133 LYS cc_start: 0.8980 (tppp) cc_final: 0.8694 (mttm) REVERT: A 281 HIS cc_start: 0.8529 (t-90) cc_final: 0.8026 (t70) REVERT: A 320 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8346 (ttm110) REVERT: A 393 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7466 (mpt-90) REVERT: A 596 THR cc_start: 0.8506 (m) cc_final: 0.8079 (p) REVERT: A 915 SER cc_start: 0.7894 (m) cc_final: 0.7604 (p) REVERT: A 1133 LEU cc_start: 0.8693 (mt) cc_final: 0.8417 (tm) REVERT: A 1218 GLN cc_start: 0.8818 (mt0) cc_final: 0.8517 (mt0) REVERT: A 1287 TYR cc_start: 0.8291 (m-10) cc_final: 0.7952 (m-10) REVERT: A 1312 ASN cc_start: 0.8104 (t0) cc_final: 0.7278 (t0) REVERT: A 1330 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8043 (p0) REVERT: A 1446 ASP cc_start: 0.7650 (t0) cc_final: 0.6961 (t0) REVERT: B 101 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8993 (mtt) REVERT: B 228 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: B 350 GLN cc_start: 0.8407 (tp40) cc_final: 0.7917 (tm-30) REVERT: B 358 LYS cc_start: 0.8689 (mttt) cc_final: 0.8237 (mmmm) REVERT: B 561 TRP cc_start: 0.8485 (m100) cc_final: 0.8260 (m100) REVERT: B 620 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: B 878 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7616 (mp10) REVERT: B 1210 MET cc_start: 0.9186 (ttm) cc_final: 0.8944 (mtm) REVERT: D 35 LEU cc_start: 0.7710 (pp) cc_final: 0.7379 (tm) REVERT: D 123 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6990 (mt) REVERT: D 214 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7602 (mp) REVERT: H 27 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7566 (mp0) REVERT: H 123 MET cc_start: 0.8982 (ttp) cc_final: 0.8666 (ttp) REVERT: H 138 GLU cc_start: 0.8294 (pm20) cc_final: 0.7923 (pm20) outliers start: 58 outliers final: 30 residues processed: 364 average time/residue: 0.7900 time to fit residues: 334.1619 Evaluate side-chains 357 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 216 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 312 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN I 22 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1025 HIS B1177 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066137 restraints weight = 57265.442| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.45 r_work: 0.2823 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 33166 Z= 0.203 Angle : 0.604 15.571 44949 Z= 0.304 Chirality : 0.045 0.219 5051 Planarity : 0.004 0.070 5690 Dihedral : 8.814 140.579 4766 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.54 % Allowed : 16.21 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3936 helix: 1.17 (0.14), residues: 1380 sheet: -0.24 (0.20), residues: 618 loop : 0.16 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 42 TYR 0.019 0.002 TYR G 51 PHE 0.027 0.002 PHE A 219 TRP 0.013 0.001 TRP B 31 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (33134) covalent geometry : angle 0.58295 / 0.30 (44904) hydrogen bonds : bond 0.03698 / 2.51 ( 1383) hydrogen bonds : angle 4.75056 / 3.36 ( 3867) metal coordination : bond 0.00900 / 0.57 ( 32) metal coordination : angle 5.08456 / 3.12 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 0.951 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: C 155 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7881 (pp) REVERT: E 3 GLN cc_start: 0.8632 (pm20) cc_final: 0.8323 (pm20) REVERT: E 7 ARG cc_start: 0.8346 (ptm160) cc_final: 0.8078 (ptp-170) REVERT: E 41 ASP cc_start: 0.8990 (m-30) cc_final: 0.8745 (m-30) REVERT: E 94 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8894 (tppp) REVERT: E 102 GLU cc_start: 0.8751 (pp20) cc_final: 0.8453 (pp20) REVERT: E 215 MET cc_start: 0.7113 (mmp) cc_final: 0.6841 (mmt) REVERT: F 110 ASP cc_start: 0.8431 (p0) cc_final: 0.8020 (p0) REVERT: F 112 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7738 (mp0) REVERT: F 114 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7434 (pt0) REVERT: G 21 ARG cc_start: 0.7989 (ppt170) cc_final: 0.7777 (ppp-140) REVERT: G 65 ASP cc_start: 0.8302 (t0) cc_final: 0.7709 (t0) REVERT: G 69 GLU cc_start: 0.7699 (pt0) cc_final: 0.6817 (pp20) REVERT: G 73 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (mtpp) REVERT: G 75 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7348 (mmt180) REVERT: G 109 PHE cc_start: 0.6666 (t80) cc_final: 0.6451 (t80) REVERT: G 115 MET cc_start: 0.3987 (mpp) cc_final: 0.3315 (mtt) REVERT: I 28 GLU cc_start: 0.8430 (tt0) cc_final: 0.8165 (tp30) REVERT: I 54 GLU cc_start: 0.7044 (pt0) cc_final: 0.6791 (pt0) REVERT: I 61 ASP cc_start: 0.8724 (p0) cc_final: 0.8459 (p0) REVERT: J 26 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8584 (mt0) REVERT: J 29 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7793 (tm-30) REVERT: K 54 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8437 (tpt170) REVERT: K 111 LEU cc_start: 0.8921 (tp) cc_final: 0.8718 (mm) REVERT: L 66 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8317 (tp40) REVERT: A 45 GLN cc_start: 0.8912 (mm110) cc_final: 0.8405 (mp10) REVERT: A 74 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8290 (mtm) REVERT: A 133 LYS cc_start: 0.8965 (tppp) cc_final: 0.8674 (mttm) REVERT: A 281 HIS cc_start: 0.8597 (t-90) cc_final: 0.8093 (t70) REVERT: A 320 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8429 (ttm110) REVERT: A 393 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7509 (mpt-90) REVERT: A 596 THR cc_start: 0.8581 (m) cc_final: 0.8202 (p) REVERT: A 915 SER cc_start: 0.7911 (m) cc_final: 0.7548 (p) REVERT: A 1133 LEU cc_start: 0.8673 (mt) cc_final: 0.8411 (tm) REVERT: A 1191 TRP cc_start: 0.8295 (m100) cc_final: 0.7689 (m100) REVERT: A 1218 GLN cc_start: 0.8852 (mt0) cc_final: 0.8614 (mt0) REVERT: A 1307 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 1312 ASN cc_start: 0.8177 (t0) cc_final: 0.7334 (t0) REVERT: A 1330 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8003 (p0) REVERT: A 1446 ASP cc_start: 0.7765 (t0) cc_final: 0.7057 (t0) REVERT: B 101 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8999 (mmt) REVERT: B 228 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (mtpp) REVERT: B 322 PHE cc_start: 0.8707 (t80) cc_final: 0.8400 (t80) REVERT: B 350 GLN cc_start: 0.8387 (tp40) cc_final: 0.7868 (tm-30) REVERT: B 358 LYS cc_start: 0.8686 (mttt) cc_final: 0.8230 (mmmm) REVERT: B 430 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7921 (mtm110) REVERT: B 434 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7391 (ttp80) REVERT: B 561 TRP cc_start: 0.8502 (m100) cc_final: 0.8279 (m100) REVERT: B 878 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7595 (mp10) REVERT: B 948 ILE cc_start: 0.8691 (mp) cc_final: 0.8442 (mp) REVERT: B 1210 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8948 (mtm) REVERT: D 35 LEU cc_start: 0.7736 (pp) cc_final: 0.7497 (tt) REVERT: D 123 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7003 (mt) REVERT: D 214 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7620 (mp) REVERT: H 11 GLN cc_start: 0.8590 (tt0) cc_final: 0.8333 (tt0) REVERT: H 27 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7636 (mp0) REVERT: H 37 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7269 (pttp) REVERT: H 123 MET cc_start: 0.9027 (ttp) cc_final: 0.8807 (ttp) REVERT: H 138 GLU cc_start: 0.8239 (pm20) cc_final: 0.7829 (pm20) outliers start: 54 outliers final: 25 residues processed: 362 average time/residue: 0.7723 time to fit residues: 325.3199 Evaluate side-chains 353 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 150 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 304 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.066308 restraints weight = 57878.008| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.45 r_work: 0.2834 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33166 Z= 0.147 Angle : 0.588 14.221 44949 Z= 0.294 Chirality : 0.043 0.200 5051 Planarity : 0.004 0.069 5690 Dihedral : 8.791 139.845 4766 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.23 % Allowed : 16.81 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3936 helix: 1.21 (0.14), residues: 1380 sheet: -0.21 (0.20), residues: 615 loop : 0.15 (0.15), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 879 TYR 0.019 0.001 TYR G 167 PHE 0.025 0.001 PHE A 219 TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (33134) covalent geometry : angle 0.56838 / 0.29 (44904) hydrogen bonds : bond 0.03498 / 2.37 ( 1383) hydrogen bonds : angle 4.69428 / 3.31 ( 3867) metal coordination : bond 0.00571 / 0.37 ( 32) metal coordination : angle 4.77637 / 2.99 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 1.298 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: C 155 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7704 (pp) REVERT: E 3 GLN cc_start: 0.8624 (pm20) cc_final: 0.8316 (pm20) REVERT: E 7 ARG cc_start: 0.8333 (ptm160) cc_final: 0.8073 (ptp-170) REVERT: E 41 ASP cc_start: 0.9003 (m-30) cc_final: 0.8653 (m-30) REVERT: E 94 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8887 (tppp) REVERT: E 102 GLU cc_start: 0.8740 (pp20) cc_final: 0.8444 (pp20) REVERT: E 112 TYR cc_start: 0.8308 (p90) cc_final: 0.7747 (p90) REVERT: E 215 MET cc_start: 0.7098 (mmp) cc_final: 0.6823 (mmt) REVERT: F 110 ASP cc_start: 0.8504 (p0) cc_final: 0.8176 (p0) REVERT: F 112 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7766 (mm-30) REVERT: G 21 ARG cc_start: 0.7947 (ppt170) cc_final: 0.7694 (ppp-140) REVERT: G 65 ASP cc_start: 0.8266 (t0) cc_final: 0.7671 (t0) REVERT: G 69 GLU cc_start: 0.7689 (pt0) cc_final: 0.6830 (pp20) REVERT: G 73 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7850 (mtpp) REVERT: G 75 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7374 (mmt180) REVERT: G 109 PHE cc_start: 0.6679 (t80) cc_final: 0.6461 (t80) REVERT: G 115 MET cc_start: 0.3909 (mpp) cc_final: 0.3274 (mtt) REVERT: I 28 GLU cc_start: 0.8349 (tt0) cc_final: 0.8144 (tp30) REVERT: I 61 ASP cc_start: 0.8695 (p0) cc_final: 0.8442 (p0) REVERT: I 89 GLN cc_start: 0.8653 (mm110) cc_final: 0.7934 (mm110) REVERT: J 29 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7732 (tm-30) REVERT: K 54 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8446 (tpt170) REVERT: L 66 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8229 (tp40) REVERT: A 45 GLN cc_start: 0.8916 (mm110) cc_final: 0.8412 (mp10) REVERT: A 74 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8299 (mtm) REVERT: A 133 LYS cc_start: 0.8968 (tppp) cc_final: 0.8726 (mttm) REVERT: A 281 HIS cc_start: 0.8612 (t-90) cc_final: 0.8112 (t70) REVERT: A 311 GLN cc_start: 0.8159 (mt0) cc_final: 0.7854 (tt0) REVERT: A 320 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8514 (ttm110) REVERT: A 393 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (mmt90) REVERT: A 486 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 596 THR cc_start: 0.8464 (m) cc_final: 0.8039 (p) REVERT: A 915 SER cc_start: 0.7833 (m) cc_final: 0.7538 (p) REVERT: A 1133 LEU cc_start: 0.8663 (mt) cc_final: 0.8417 (tm) REVERT: A 1218 GLN cc_start: 0.8872 (mt0) cc_final: 0.8567 (mt0) REVERT: A 1284 MET cc_start: 0.8543 (ttm) cc_final: 0.8282 (ttm) REVERT: A 1312 ASN cc_start: 0.8092 (t0) cc_final: 0.7390 (t0) REVERT: A 1330 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8011 (p0) REVERT: A 1446 ASP cc_start: 0.7621 (t0) cc_final: 0.7064 (t0) REVERT: B 101 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.9010 (mmt) REVERT: B 228 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: B 322 PHE cc_start: 0.8724 (t80) cc_final: 0.8428 (t80) REVERT: B 350 GLN cc_start: 0.8386 (tp40) cc_final: 0.7892 (tm-30) REVERT: B 358 LYS cc_start: 0.8694 (mttt) cc_final: 0.8236 (mmmm) REVERT: B 430 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7951 (mtm110) REVERT: B 434 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7439 (ttp80) REVERT: B 561 TRP cc_start: 0.8517 (m100) cc_final: 0.8255 (m100) REVERT: B 620 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.7884 (mmm-85) REVERT: B 1210 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8933 (mtm) REVERT: D 35 LEU cc_start: 0.7654 (pp) cc_final: 0.7338 (tm) REVERT: D 123 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (mt) REVERT: D 214 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7595 (mp) REVERT: D 219 THR cc_start: 0.5831 (OUTLIER) cc_final: 0.5460 (t) REVERT: H 11 GLN cc_start: 0.8602 (tt0) cc_final: 0.8349 (tt0) REVERT: H 27 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7707 (mp0) REVERT: H 37 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7364 (pttp) REVERT: H 103 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7974 (ttpt) REVERT: H 123 MET cc_start: 0.9020 (ttp) cc_final: 0.8810 (ttp) REVERT: H 138 GLU cc_start: 0.8225 (pm20) cc_final: 0.7810 (pm20) outliers start: 43 outliers final: 23 residues processed: 351 average time/residue: 0.7585 time to fit residues: 310.9250 Evaluate side-chains 352 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 223 optimal weight: 0.0970 chunk 387 optimal weight: 0.0470 chunk 154 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 109 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 5 ASN E 101 GLN J 23 ASN J 26 GLN A 4 GLN A1048 ASN B 887 HIS B1177 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068363 restraints weight = 57449.288| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.45 r_work: 0.2880 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33166 Z= 0.108 Angle : 0.566 13.166 44949 Z= 0.284 Chirality : 0.042 0.186 5051 Planarity : 0.004 0.069 5690 Dihedral : 8.732 138.480 4766 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.23 % Allowed : 17.04 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3936 helix: 1.32 (0.14), residues: 1374 sheet: -0.13 (0.21), residues: 606 loop : 0.18 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 130 TYR 0.032 0.001 TYR B 666 PHE 0.023 0.001 PHE A 219 TRP 0.012 0.001 TRP C 201 HIS 0.003 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (33134) covalent geometry : angle 0.55127 / 0.28 (44904) hydrogen bonds : bond 0.03250 / 2.20 ( 1383) hydrogen bonds : angle 4.58017 / 3.23 ( 3867) metal coordination : bond 0.00401 / 0.26 ( 32) metal coordination : angle 4.04471 / 2.55 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14514.75 seconds wall clock time: 247 minutes 18.51 seconds (14838.51 seconds total)