Starting phenix.real_space_refine on Mon Jul 6 10:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x75_33032/07_2026/7x75_33032.cif" } resolution = 3.45 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= 0.003 sd= 0.045 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 20 6.06 5 P 168 5.49 5 Mg 1 5.21 5 S 126 5.16 5 C 21252 2.51 5 N 6265 2.21 5 O 7040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "K" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1730 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 70.811 109.205 112.275 1.00 69.88 S ATOM 12691 SG CYS D 62 69.812 110.590 115.538 1.00 77.34 S ATOM 12800 SG CYS D 75 73.632 110.140 114.908 1.00 78.06 S ATOM 12826 SG CYS D 78 71.661 107.268 115.513 1.00 70.79 S ATOM 19225 SG CYS D 886 110.141 61.388 84.195 1.00 68.68 S ATOM 19789 SG CYS D 962 106.742 61.472 85.616 1.00 58.06 S ATOM 19837 SG CYS D 969 107.117 62.924 82.086 1.00 48.20 S ATOM 19856 SG CYS D 972 107.243 59.327 82.557 1.00 51.55 S ATOM 25721 SG CYS G 90 60.544 186.295 77.538 1.00151.17 S ATOM 25743 SG CYS G 93 58.009 187.154 74.858 1.00151.76 S ATOM 26016 SG CYS G 130 58.272 188.890 78.433 1.00148.17 S ATOM 26035 SG CYS G 133 56.616 185.557 77.922 1.00145.54 S ATOM 25635 SG CYS G 79 73.073 195.180 74.893 1.00156.90 S ATOM 26705 SG CYS H 90 92.044 179.962 92.468 1.00152.25 S ATOM 26727 SG CYS H 93 94.353 177.963 94.695 1.00152.19 S ATOM 27000 SG CYS H 130 93.317 181.547 95.638 1.00151.24 S ATOM 27019 SG CYS H 133 95.887 180.649 92.785 1.00148.20 S ATOM 26619 SG CYS H 79 77.112 174.673 98.346 1.00146.86 S ATOM 27689 SG CYS K 90 123.927 185.058 53.705 1.00147.97 S ATOM 27711 SG CYS K 93 124.337 181.621 52.609 1.00147.71 S ATOM 27984 SG CYS K 130 127.134 183.328 54.686 1.00149.28 S ATOM 28003 SG CYS K 133 126.497 183.773 50.798 1.00144.47 S ATOM 27603 SG CYS K 79 115.395 183.780 67.107 1.00154.91 S ATOM 28673 SG CYS L 90 102.905 210.620 66.809 1.00144.73 S ATOM 28695 SG CYS L 93 101.310 213.960 67.147 1.00143.14 S ATOM 28968 SG CYS L 130 103.458 212.752 70.075 1.00148.05 S ATOM 28987 SG CYS L 133 100.077 211.151 69.311 1.00145.74 S ATOM 28587 SG CYS L 79 115.832 213.015 55.960 1.00153.69 S ATOM 29657 SG CYS M 90 65.428 172.892 34.927 1.00151.94 S ATOM 29679 SG CYS M 93 61.910 173.510 36.440 1.00146.63 S ATOM 29952 SG CYS M 130 62.364 171.558 33.199 1.00149.24 S ATOM 29971 SG CYS M 133 62.941 175.353 33.376 1.00144.40 S ATOM 29571 SG CYS M 79 67.748 158.586 41.585 1.00156.09 S ATOM 30641 SG CYS N 90 95.360 155.557 35.537 1.00143.45 S ATOM 30663 SG CYS N 93 99.203 155.372 35.650 1.00141.51 S ATOM 30936 SG CYS N 130 97.192 153.747 32.826 1.00141.95 S ATOM 30955 SG CYS N 133 97.203 152.279 36.340 1.00137.43 S ATOM 30555 SG CYS N 79 93.075 166.763 24.850 1.00151.94 S Time building chain proxies: 7.87, per 1000 atoms: 0.23 Number of scatterers: 34872 At special positions: 0 Unit cell: (142.8, 229.95, 200.55, 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 20 29.99 S 126 16.00 P 168 15.00 Mg 1 11.99 O 7040 8.00 N 6265 7.00 C 21252 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: 2.71 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 93 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 130 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 133 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 85 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 79 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 87 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 122 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 86 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 84 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 93 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 133 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 130 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 85 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 87 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 79 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 86 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 84 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 48 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7468 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 47 sheets defined 44.9% alpha, 14.4% beta 62 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.764A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.705A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 4.173A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.569A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.655A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.741A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.627A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.024A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.536A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.334A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.953A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.587A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.755A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.171A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.787A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.790A pdb=" N GLU D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.776A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 227 removed outlier: 3.775A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.641A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.563A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.663A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.854A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.572A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.950A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 3.516A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 530 removed outlier: 3.573A pdb=" N CYS D 529 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 525 through 530' Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.705A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.877A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.711A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.887A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.803A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.785A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.556A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.634A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 Processing helix chain 'D' and resid 1109 through 1127 Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.946A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1209 removed outlier: 3.569A pdb=" N SER D1208 " --> pdb=" O LEU D1204 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1223 removed outlier: 3.798A pdb=" N VAL D1215 " --> pdb=" O GLU D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1237 Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.161A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 45 removed outlier: 3.535A pdb=" N LEU E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.976A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 299 through 318 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.678A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.577A pdb=" N LEU F 386 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.764A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 479 removed outlier: 3.669A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 479 " --> pdb=" O ILE F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 498 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.113A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.831A pdb=" N ALA G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 48 through 62 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.529A pdb=" N GLU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 115 removed outlier: 3.764A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.214A pdb=" N ALA H 134 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 135' Processing helix chain 'K' and resid 13 through 26 Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 47 through 62 Processing helix chain 'K' and resid 101 through 115 removed outlier: 3.692A pdb=" N GLU K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 4.096A pdb=" N ALA K 134 " --> pdb=" O CYS K 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 130 through 135' Processing helix chain 'L' and resid 13 through 25 Processing helix chain 'L' and resid 32 through 43 Processing helix chain 'L' and resid 48 through 62 Processing helix chain 'L' and resid 101 through 115 removed outlier: 3.828A pdb=" N GLU L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 removed outlier: 3.636A pdb=" N ALA L 134 " --> pdb=" O CYS L 130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'M' and resid 13 through 26 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.924A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 31 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.195A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.162A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 255 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 271 through 278 Processing helix chain 'S' and resid 279 through 286 removed outlier: 3.536A pdb=" N ILE S 286 " --> pdb=" O ASP S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 304 removed outlier: 3.751A pdb=" N MET S 304 " --> pdb=" O LYS S 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.481A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.990A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.670A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.693A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.603A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.532A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.339A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.486A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 142 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 129 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.502A pdb=" N GLN C 166 " --> pdb=" O ARG C 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.667A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 removed outlier: 3.510A pdb=" N THR C 341 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 440 through 442 removed outlier: 3.703A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.787A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.859A pdb=" N ASP C 566 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 5.857A pdb=" N VAL C 636 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR C 647 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 638 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.298A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.686A pdb=" N HIS C 741 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 3.887A pdb=" N VAL C 789 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 930 through 931 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.842A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.649A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.689A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.504A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AD6, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD8, first strand: chain 'D' and resid 892 through 894 removed outlier: 3.907A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.573A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE2, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.505A pdb=" N ARG D1254 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AE4, first strand: chain 'G' and resid 96 through 99 removed outlier: 5.207A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE G 127 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS H 87 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE H 126 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL H 89 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 128 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'K' and resid 64 through 68 Processing sheet with id=AE7, first strand: chain 'K' and resid 96 through 99 removed outlier: 4.955A pdb=" N HIS K 87 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE K 126 " --> pdb=" O HIS K 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE K 127 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS L 87 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE L 126 " --> pdb=" O HIS L 87 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 89 " --> pdb=" O ILE L 126 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY L 128 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.832A pdb=" N ARG L 30 " --> pdb=" O TYR L 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 65 through 68 removed outlier: 3.611A pdb=" N ARG M 77 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.133A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS N 87 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 65 through 68 1492 hydrogen bonds defined for protein. 4263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 165 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 3.65 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: 11080 1.34 - 1.46: 6055 1.46 - 1.58: 18104 1.58 - 1.70: 334 1.70 - 1.82: 206 Bond restraints: 35779 Sorted by residual: bond pdb=" C1' DC O 8 " pdb=" N1 DC O 8 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DC O 83 " pdb=" N1 DC O 83 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" C3' DT O 19 " pdb=" C2' DT O 19 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.27e+01 bond pdb=" C1' DC P 67 " pdb=" N1 DC P 67 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C1' DC O 84 " pdb=" N1 DC O 84 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.03e+01 ... (remaining 35774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 47901 2.29 - 4.58: 1091 4.58 - 6.87: 102 6.87 - 9.16: 20 9.16 - 11.45: 5 Bond angle restraints: 49119 Sorted by residual: angle pdb=" N ARG C1029 " pdb=" CA ARG C1029 " pdb=" C ARG C1029 " ideal model delta sigma weight residual 107.20 118.65 -11.45 1.70e+00 3.46e-01 4.53e+01 angle pdb=" N LYS D 64 " pdb=" CA LYS D 64 " pdb=" C LYS D 64 " ideal model delta sigma weight residual 111.07 117.38 -6.31 1.07e+00 8.73e-01 3.48e+01 angle pdb=" N THR D1213 " pdb=" CA THR D1213 " pdb=" C THR D1213 " ideal model delta sigma weight residual 111.07 116.98 -5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" N SER A 44 " pdb=" CA SER A 44 " pdb=" C SER A 44 " ideal model delta sigma weight residual 111.07 116.64 -5.57 1.07e+00 8.73e-01 2.71e+01 angle pdb=" N THR D1212 " pdb=" CA THR D1212 " pdb=" C THR D1212 " ideal model delta sigma weight residual 111.36 116.85 -5.49 1.09e+00 8.42e-01 2.54e+01 ... (remaining 49114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 20132 35.66 - 71.32: 1135 71.32 - 106.98: 49 106.98 - 142.65: 3 142.65 - 178.31: 14 Dihedral angle restraints: 21333 sinusoidal: 9732 harmonic: 11601 Sorted by residual: dihedral pdb=" C VAL C 908 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " pdb=" CB VAL C 908 " ideal model delta harmonic sigma weight residual -122.00 -133.45 11.45 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C4' DT P 76 " pdb=" C3' DT P 76 " pdb=" O3' DT P 76 " pdb=" P DG P 77 " ideal model delta sinusoidal sigma weight residual -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT P 73 " pdb=" C3' DT P 73 " pdb=" O3' DT P 73 " pdb=" P DC P 74 " ideal model delta sinusoidal sigma weight residual 220.00 46.97 173.03 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 21330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4955 0.083 - 0.166: 583 0.166 - 0.249: 34 0.249 - 0.331: 4 0.331 - 0.414: 5 Chirality restraints: 5581 Sorted by residual: chirality pdb=" C3' DG O 20 " pdb=" C4' DG O 20 " pdb=" O3' DG O 20 " pdb=" C2' DG O 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C3' DG O 72 " pdb=" C4' DG O 72 " pdb=" O3' DG O 72 " pdb=" C2' DG O 72 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C3' DT P 73 " pdb=" C4' DT P 73 " pdb=" O3' DT P 73 " pdb=" C2' DT P 73 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5578 not shown) Planarity restraints: 5854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 215 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CG ASP C 215 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP C 215 " -0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP C 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 593 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C GLU D 593 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU D 593 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY D 594 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 474 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO C 475 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 475 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 475 " -0.037 5.00e-02 4.00e+02 ... (remaining 5851 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 257 2.55 - 3.14: 28413 3.14 - 3.73: 57983 3.73 - 4.31: 75165 4.31 - 4.90: 122773 Nonbonded interactions: 284591 Sorted by model distance: nonbonded pdb=" OD2 ASP L 65 " pdb="ZN ZN L 202 " model vdw 1.963 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.969 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.997 2.230 nonbonded pdb=" OD2 ASP K 65 " pdb="ZN ZN K 202 " model vdw 2.015 2.230 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 2.020 2.170 ... (remaining 284586 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.007 0.413 35847 Z= 0.353 Angle : 0.793 11.448 49167 Z= 0.487 Chirality : 0.051 0.414 5581 Planarity : 0.004 0.086 5854 Dihedral : 19.863 178.307 13865 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.66 % Allowed : 19.99 % Favored : 79.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.13), residues: 4029 helix: 1.31 (0.13), residues: 1656 sheet: -0.44 (0.24), residues: 459 loop : -0.39 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 245 TYR 0.029 0.001 TYR E 32 PHE 0.037 0.002 PHE D 252 TRP 0.023 0.001 TRP C 199 HIS 0.012 0.001 HIS H 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.32 (35779) covalent geometry : angle 0.77814 / 0.49 (49119) hydrogen bonds : bond 0.16423 / 11.23 ( 1655) hydrogen bonds : angle 6.01347 / 4.20 ( 4593) metal coordination : bond 0.10687 / 8.48 ( 68) metal coordination : angle 4.99408 / 3.08 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 362 time to evaluate : 1.127 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: B 152 ASN cc_start: 0.6902 (m-40) cc_final: 0.6480 (p0) REVERT: D 70 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6293 (p90) REVERT: D 609 GLU cc_start: 0.8343 (tt0) cc_final: 0.8133 (tt0) REVERT: D 1077 ARG cc_start: 0.6147 (ptm-80) cc_final: 0.5700 (ttp80) REVERT: N 38 MET cc_start: 0.1479 (tmm) cc_final: 0.0664 (ptt) outliers start: 22 outliers final: 9 residues processed: 381 average time/residue: 0.2196 time to fit residues: 135.2019 Evaluate side-chains 290 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 280 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain G residue 79 CYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN B 82 GLN C 424 GLN C 429 ASN C 980 ASN C1040 GLN D 213 GLN D 669 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.193390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142047 restraints weight = 58276.403| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.56 r_work: 0.3417 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35847 Z= 0.155 Angle : 0.682 11.793 49167 Z= 0.363 Chirality : 0.046 0.384 5581 Planarity : 0.005 0.061 5854 Dihedral : 20.124 179.603 6234 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.42 % Allowed : 18.53 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.13), residues: 4029 helix: 1.24 (0.12), residues: 1673 sheet: -0.24 (0.23), residues: 469 loop : -0.45 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 56 TYR 0.021 0.001 TYR E 32 PHE 0.020 0.002 PHE F 462 TRP 0.032 0.001 TRP F 333 HIS 0.034 0.001 HIS L 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (35779) covalent geometry : angle 0.66755 / 0.36 (49119) hydrogen bonds : bond 0.05085 / 3.48 ( 1655) hydrogen bonds : angle 4.78670 / 3.35 ( 4593) metal coordination : bond 0.01093 / 0.80 ( 68) metal coordination : angle 4.52734 / 2.87 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 1.439 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: B 96 TYR cc_start: 0.6815 (m-10) cc_final: 0.6605 (m-10) REVERT: B 134 LEU cc_start: 0.7889 (tp) cc_final: 0.7686 (pp) REVERT: B 152 ASN cc_start: 0.7595 (m-40) cc_final: 0.6661 (p0) REVERT: C 136 LYS cc_start: 0.7272 (ptpt) cc_final: 0.6908 (pttt) REVERT: C 142 MET cc_start: 0.6979 (ppp) cc_final: 0.6586 (ppp) REVERT: C 442 ASN cc_start: 0.9147 (t0) cc_final: 0.8828 (t0) REVERT: D 241 TYR cc_start: 0.8586 (t80) cc_final: 0.8059 (t80) REVERT: D 825 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: D 889 GLU cc_start: 0.7148 (tp30) cc_final: 0.6806 (tp30) REVERT: D 1077 ARG cc_start: 0.6820 (ptm-80) cc_final: 0.6136 (ttp80) REVERT: F 277 HIS cc_start: 0.8596 (m-70) cc_final: 0.8385 (m170) REVERT: F 499 HIS cc_start: 0.8590 (t-90) cc_final: 0.8272 (t-90) REVERT: G 38 MET cc_start: 0.4294 (ppp) cc_final: 0.3508 (pmm) outliers start: 81 outliers final: 36 residues processed: 396 average time/residue: 0.2100 time to fit residues: 138.4657 Evaluate side-chains 310 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1107 ILE Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 53 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 263 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 227 optimal weight: 0.0000 chunk 354 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 394 optimal weight: 50.0000 chunk 295 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 316 optimal weight: 1.9990 chunk 412 optimal weight: 30.0000 chunk 393 optimal weight: 30.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN C1040 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN D 384 ASN D 416 ASN D1021 GLN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN F 488 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.190125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137373 restraints weight = 57907.446| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.83 r_work: 0.3348 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35847 Z= 0.206 Angle : 0.685 14.296 49167 Z= 0.362 Chirality : 0.047 0.355 5581 Planarity : 0.005 0.070 5854 Dihedral : 20.170 177.472 6227 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.94 % Allowed : 18.32 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.13), residues: 4029 helix: 1.16 (0.12), residues: 1672 sheet: -0.27 (0.23), residues: 465 loop : -0.61 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 282 TYR 0.032 0.002 TYR E 32 PHE 0.026 0.002 PHE D 248 TRP 0.029 0.002 TRP C 199 HIS 0.008 0.001 HIS N 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (35779) covalent geometry : angle 0.66779 / 0.36 (49119) hydrogen bonds : bond 0.04863 / 3.34 ( 1655) hydrogen bonds : angle 4.61754 / 3.25 ( 4593) metal coordination : bond 0.00575 / 0.39 ( 68) metal coordination : angle 4.94412 / 3.30 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 303 time to evaluate : 1.312 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: A 109 ASP cc_start: 0.8042 (t0) cc_final: 0.7751 (t0) REVERT: A 146 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 43 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 70 LYS cc_start: 0.8597 (tptt) cc_final: 0.7870 (tptt) REVERT: B 110 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 151 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8276 (tm-30) REVERT: B 152 ASN cc_start: 0.7500 (m-40) cc_final: 0.6572 (p0) REVERT: C 57 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7852 (tpp80) REVERT: C 142 MET cc_start: 0.7154 (ppp) cc_final: 0.6862 (ppp) REVERT: C 442 ASN cc_start: 0.9116 (t0) cc_final: 0.8835 (t0) REVERT: C 503 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7811 (ttm170) REVERT: C 1048 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: C 1102 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7038 (pt) REVERT: D 70 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7127 (p90) REVERT: D 73 ILE cc_start: 0.7804 (pt) cc_final: 0.7522 (pt) REVERT: D 312 MET cc_start: 0.8538 (mmt) cc_final: 0.8131 (mmt) REVERT: D 580 ASP cc_start: 0.8107 (t0) cc_final: 0.7868 (t0) REVERT: D 825 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: D 1077 ARG cc_start: 0.6865 (ptm-80) cc_final: 0.6206 (ttp80) REVERT: E 12 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7261 (pt) REVERT: F 277 HIS cc_start: 0.8607 (m-70) cc_final: 0.8377 (m170) REVERT: F 386 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8519 (pp) REVERT: F 388 MET cc_start: 0.7201 (mpp) cc_final: 0.6967 (mpp) REVERT: N 38 MET cc_start: 0.2025 (ptt) cc_final: 0.1579 (pmm) outliers start: 132 outliers final: 69 residues processed: 405 average time/residue: 0.1997 time to fit residues: 135.5368 Evaluate side-chains 345 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1095 GLU Chi-restraints excluded: chain C residue 1102 ILE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 384 ASN Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1107 ILE Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 81 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 215 optimal weight: 0.0670 chunk 311 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 295 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN C 374 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 916 GLN C1040 GLN D 35 ASN D 213 GLN D 384 ASN D 440 GLN F 252 ASN F 371 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.191058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138308 restraints weight = 57496.401| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.83 r_work: 0.3364 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35847 Z= 0.160 Angle : 0.648 12.295 49167 Z= 0.342 Chirality : 0.046 0.314 5581 Planarity : 0.004 0.064 5854 Dihedral : 20.146 177.304 6227 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 19.72 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.13), residues: 4029 helix: 1.26 (0.12), residues: 1677 sheet: -0.29 (0.23), residues: 476 loop : -0.58 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 282 TYR 0.034 0.001 TYR E 32 PHE 0.029 0.002 PHE D 248 TRP 0.019 0.001 TRP F 333 HIS 0.006 0.001 HIS C 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (35779) covalent geometry : angle 0.63340 / 0.34 (49119) hydrogen bonds : bond 0.04381 / 3.01 ( 1655) hydrogen bonds : angle 4.47062 / 3.15 ( 4593) metal coordination : bond 0.00511 / 0.40 ( 68) metal coordination : angle 4.39720 / 2.91 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 295 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.8025 (t0) cc_final: 0.7682 (t0) REVERT: A 146 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.6688 (t80) REVERT: A 151 GLN cc_start: 0.7492 (pm20) cc_final: 0.7223 (pm20) REVERT: B 43 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8113 (mp) REVERT: B 70 LYS cc_start: 0.8614 (tptt) cc_final: 0.8000 (tptt) REVERT: B 151 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 152 ASN cc_start: 0.7511 (m-40) cc_final: 0.6520 (p0) REVERT: C 142 MET cc_start: 0.7085 (ppp) cc_final: 0.6648 (ppp) REVERT: C 442 ASN cc_start: 0.9111 (t0) cc_final: 0.8847 (t0) REVERT: C 503 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: C 522 GLU cc_start: 0.7590 (tt0) cc_final: 0.7377 (tt0) REVERT: C 753 GLU cc_start: 0.7860 (mp0) cc_final: 0.7607 (mp0) REVERT: C 1048 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: D 205 MET cc_start: 0.8912 (mtt) cc_final: 0.8682 (mtt) REVERT: D 312 MET cc_start: 0.8514 (mmt) cc_final: 0.8156 (mmt) REVERT: D 825 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: D 919 MET cc_start: 0.7712 (mmm) cc_final: 0.7078 (mmm) REVERT: D 1077 ARG cc_start: 0.6833 (ptm-80) cc_final: 0.6396 (ttp80) REVERT: E 12 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7234 (pt) REVERT: F 277 HIS cc_start: 0.8605 (m-70) cc_final: 0.8353 (m170) REVERT: F 320 TYR cc_start: 0.8041 (p90) cc_final: 0.7754 (p90) REVERT: F 324 TYR cc_start: 0.8284 (m-80) cc_final: 0.8070 (m-80) REVERT: F 386 LEU cc_start: 0.8848 (pt) cc_final: 0.8355 (pp) REVERT: F 499 HIS cc_start: 0.8583 (t-90) cc_final: 0.8265 (t-90) REVERT: N 38 MET cc_start: 0.1884 (ptt) cc_final: 0.1116 (ppp) outliers start: 105 outliers final: 70 residues processed: 377 average time/residue: 0.2062 time to fit residues: 130.7119 Evaluate side-chains 354 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 113 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 358 optimal weight: 50.0000 chunk 332 optimal weight: 7.9990 chunk 385 optimal weight: 50.0000 chunk 221 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 885 ASN C1040 GLN D 213 GLN F 371 GLN ** F 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN L 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.190230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137268 restraints weight = 57471.259| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.81 r_work: 0.3358 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.499 35847 Z= 0.189 Angle : 0.639 12.258 49167 Z= 0.336 Chirality : 0.046 0.317 5581 Planarity : 0.004 0.055 5854 Dihedral : 20.097 177.686 6227 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.64 % Allowed : 19.78 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.13), residues: 4029 helix: 1.34 (0.13), residues: 1677 sheet: -0.36 (0.23), residues: 487 loop : -0.58 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 282 TYR 0.035 0.001 TYR E 32 PHE 0.030 0.002 PHE D 248 TRP 0.018 0.001 TRP C 199 HIS 0.011 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (35779) covalent geometry : angle 0.62474 / 0.34 (49119) hydrogen bonds : bond 0.04269 / 2.93 ( 1655) hydrogen bonds : angle 4.39346 / 3.09 ( 4593) metal coordination : bond 0.06100 / 5.13 ( 68) metal coordination : angle 4.30290 / 2.88 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 299 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7999 (t0) cc_final: 0.7737 (t0) REVERT: A 146 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6725 (t80) REVERT: A 151 GLN cc_start: 0.7551 (pm20) cc_final: 0.7250 (pm20) REVERT: B 43 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 70 LYS cc_start: 0.8598 (tptt) cc_final: 0.7991 (tptt) REVERT: B 151 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 152 ASN cc_start: 0.7223 (m-40) cc_final: 0.6340 (p0) REVERT: C 142 MET cc_start: 0.7146 (ppp) cc_final: 0.6627 (ppp) REVERT: C 503 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7833 (ttm170) REVERT: C 522 GLU cc_start: 0.7612 (tt0) cc_final: 0.7300 (tt0) REVERT: C 753 GLU cc_start: 0.7956 (mp0) cc_final: 0.7643 (mp0) REVERT: C 1048 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: D 205 MET cc_start: 0.8836 (mtt) cc_final: 0.8549 (mtt) REVERT: D 312 MET cc_start: 0.8554 (mmt) cc_final: 0.8235 (mmt) REVERT: D 825 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: D 1077 ARG cc_start: 0.6771 (ptm-80) cc_final: 0.6375 (ttp80) REVERT: E 12 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7291 (pt) REVERT: F 277 HIS cc_start: 0.8602 (m-70) cc_final: 0.8343 (m170) REVERT: F 320 TYR cc_start: 0.8030 (p90) cc_final: 0.7739 (p90) REVERT: F 461 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8471 (tpt90) REVERT: F 499 HIS cc_start: 0.8587 (t-90) cc_final: 0.8267 (t-90) REVERT: N 38 MET cc_start: 0.1847 (ptt) cc_final: 0.1187 (ppp) outliers start: 122 outliers final: 84 residues processed: 390 average time/residue: 0.1974 time to fit residues: 129.7735 Evaluate side-chains 372 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1095 GLU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 325 optimal weight: 0.6980 chunk 411 optimal weight: 50.0000 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 0.0670 chunk 261 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1040 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN F 488 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.189325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136472 restraints weight = 57083.968| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 4.03 r_work: 0.3319 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35847 Z= 0.189 Angle : 0.656 13.809 49167 Z= 0.343 Chirality : 0.046 0.320 5581 Planarity : 0.004 0.057 5854 Dihedral : 20.102 176.899 6227 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.79 % Allowed : 20.53 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.13), residues: 4029 helix: 1.29 (0.13), residues: 1682 sheet: -0.32 (0.23), residues: 493 loop : -0.65 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 282 TYR 0.036 0.002 TYR E 32 PHE 0.031 0.002 PHE D 248 TRP 0.032 0.002 TRP C 199 HIS 0.008 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (35779) covalent geometry : angle 0.64142 / 0.34 (49119) hydrogen bonds : bond 0.04286 / 2.94 ( 1655) hydrogen bonds : angle 4.38937 / 3.08 ( 4593) metal coordination : bond 0.00673 / 0.50 ( 68) metal coordination : angle 4.38739 / 2.95 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 304 time to evaluate : 1.258 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: symmetry clash REVERT: A 109 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7849 (t0) REVERT: A 146 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.6763 (t80) REVERT: A 151 GLN cc_start: 0.7615 (pm20) cc_final: 0.7309 (pm20) REVERT: B 43 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 70 LYS cc_start: 0.8631 (tptt) cc_final: 0.7991 (tptt) REVERT: B 151 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 152 ASN cc_start: 0.7602 (m-40) cc_final: 0.6621 (p0) REVERT: C 142 MET cc_start: 0.7361 (ppp) cc_final: 0.6766 (ppp) REVERT: C 293 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8330 (tpp80) REVERT: C 401 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 503 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7830 (ttm170) REVERT: C 522 GLU cc_start: 0.7716 (tt0) cc_final: 0.7434 (tt0) REVERT: C 673 LYS cc_start: 0.8558 (mptt) cc_final: 0.8338 (mppt) REVERT: C 753 GLU cc_start: 0.7961 (mp0) cc_final: 0.7614 (mp0) REVERT: C 1048 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: D 205 MET cc_start: 0.8920 (mtt) cc_final: 0.8652 (mtt) REVERT: D 229 LEU cc_start: 0.6383 (mt) cc_final: 0.6101 (mt) REVERT: D 312 MET cc_start: 0.8521 (mmt) cc_final: 0.8145 (mmt) REVERT: D 872 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 919 MET cc_start: 0.7810 (mmm) cc_final: 0.7195 (mmm) REVERT: D 1006 MET cc_start: 0.4721 (ttt) cc_final: 0.4190 (ttt) REVERT: D 1077 ARG cc_start: 0.6892 (ptm-80) cc_final: 0.6451 (ttp80) REVERT: E 12 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7403 (pt) REVERT: F 277 HIS cc_start: 0.8613 (m-70) cc_final: 0.8371 (m170) REVERT: F 282 ASN cc_start: 0.8109 (m110) cc_final: 0.7877 (m-40) REVERT: F 320 TYR cc_start: 0.8006 (p90) cc_final: 0.7692 (p90) REVERT: F 386 LEU cc_start: 0.8934 (pt) cc_final: 0.8615 (pp) REVERT: F 388 MET cc_start: 0.7626 (mpp) cc_final: 0.7289 (mpp) REVERT: N 38 MET cc_start: 0.2130 (ptt) cc_final: 0.1533 (ppp) outliers start: 127 outliers final: 92 residues processed: 400 average time/residue: 0.1997 time to fit residues: 133.3826 Evaluate side-chains 383 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 284 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1013 MET Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 235 optimal weight: 0.5980 chunk 355 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 213 optimal weight: 0.2980 chunk 150 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1040 GLN D 213 GLN ** D 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN F 488 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.189505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134819 restraints weight = 57269.187| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 4.08 r_work: 0.3315 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35847 Z= 0.170 Angle : 0.643 12.555 49167 Z= 0.337 Chirality : 0.045 0.324 5581 Planarity : 0.004 0.072 5854 Dihedral : 20.095 176.507 6227 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.76 % Allowed : 21.63 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.13), residues: 4029 helix: 1.32 (0.13), residues: 1679 sheet: -0.28 (0.23), residues: 489 loop : -0.62 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 282 TYR 0.037 0.001 TYR D 134 PHE 0.032 0.002 PHE D 248 TRP 0.048 0.002 TRP D 651 HIS 0.007 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (35779) covalent geometry : angle 0.62973 / 0.34 (49119) hydrogen bonds : bond 0.04188 / 2.87 ( 1655) hydrogen bonds : angle 4.34686 / 3.04 ( 4593) metal coordination : bond 0.00454 / 0.33 ( 68) metal coordination : angle 4.13923 / 2.81 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 299 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 151 GLN cc_start: 0.7803 (pm20) cc_final: 0.7537 (pm20) REVERT: B 43 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 70 LYS cc_start: 0.8689 (tptt) cc_final: 0.8111 (tptt) REVERT: B 151 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8163 (tm-30) REVERT: B 152 ASN cc_start: 0.7543 (m-40) cc_final: 0.6563 (p0) REVERT: C 55 LYS cc_start: 0.8462 (pttm) cc_final: 0.7780 (ptpp) REVERT: C 142 MET cc_start: 0.7371 (ppp) cc_final: 0.6781 (ppp) REVERT: C 199 TRP cc_start: 0.4462 (p-90) cc_final: 0.4155 (p-90) REVERT: C 503 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7764 (ttm170) REVERT: C 522 GLU cc_start: 0.7713 (tt0) cc_final: 0.7456 (tt0) REVERT: C 753 GLU cc_start: 0.8034 (mp0) cc_final: 0.7680 (mp0) REVERT: C 1048 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: D 205 MET cc_start: 0.8879 (mtt) cc_final: 0.8602 (mtt) REVERT: D 229 LEU cc_start: 0.6413 (mt) cc_final: 0.6133 (mt) REVERT: D 312 MET cc_start: 0.8577 (mmt) cc_final: 0.8237 (mmt) REVERT: D 825 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: D 846 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8645 (mt) REVERT: D 872 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8883 (mt) REVERT: D 1077 ARG cc_start: 0.6993 (ptm-80) cc_final: 0.6545 (ttp80) REVERT: E 12 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7457 (pt) REVERT: E 49 GLU cc_start: 0.2301 (OUTLIER) cc_final: 0.2064 (pm20) REVERT: F 277 HIS cc_start: 0.8623 (m-70) cc_final: 0.8383 (m170) REVERT: F 282 ASN cc_start: 0.8121 (m110) cc_final: 0.7897 (m-40) REVERT: F 320 TYR cc_start: 0.7974 (p90) cc_final: 0.7636 (p90) REVERT: F 324 TYR cc_start: 0.8060 (m-80) cc_final: 0.7759 (m-80) REVERT: F 326 PHE cc_start: 0.7013 (t80) cc_final: 0.6683 (t80) REVERT: F 386 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8620 (pp) REVERT: F 388 MET cc_start: 0.7738 (mpp) cc_final: 0.7465 (mpp) REVERT: G 38 MET cc_start: 0.4171 (ppp) cc_final: 0.3330 (pmm) REVERT: N 38 MET cc_start: 0.1953 (ptt) cc_final: 0.1453 (ppp) outliers start: 126 outliers final: 89 residues processed: 399 average time/residue: 0.2024 time to fit residues: 136.3803 Evaluate side-chains 375 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 276 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1092 VAL Chi-restraints excluded: chain C residue 1095 GLU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 385 optimal weight: 50.0000 chunk 240 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 368 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 340 optimal weight: 50.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1040 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 384 ASN ** D 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.189584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137519 restraints weight = 57098.827| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.75 r_work: 0.3333 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35847 Z= 0.166 Angle : 0.658 12.232 49167 Z= 0.343 Chirality : 0.046 0.326 5581 Planarity : 0.004 0.059 5854 Dihedral : 20.083 176.075 6227 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.94 % Allowed : 21.72 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.13), residues: 4029 helix: 1.34 (0.13), residues: 1685 sheet: -0.26 (0.23), residues: 481 loop : -0.62 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 113 TYR 0.037 0.001 TYR E 32 PHE 0.031 0.002 PHE D 248 TRP 0.066 0.002 TRP D 651 HIS 0.007 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (35779) covalent geometry : angle 0.64589 / 0.34 (49119) hydrogen bonds : bond 0.04125 / 2.83 ( 1655) hydrogen bonds : angle 4.32149 / 3.03 ( 4593) metal coordination : bond 0.00425 / 0.29 ( 68) metal coordination : angle 4.01757 / 2.70 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 285 time to evaluate : 1.219 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: A 146 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.6737 (t80) REVERT: A 151 GLN cc_start: 0.7726 (pm20) cc_final: 0.7452 (pm20) REVERT: A 165 ASP cc_start: 0.8613 (p0) cc_final: 0.7062 (p0) REVERT: B 43 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 70 LYS cc_start: 0.8688 (tptt) cc_final: 0.8124 (tptt) REVERT: B 151 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 152 ASN cc_start: 0.7651 (m-40) cc_final: 0.6811 (p0) REVERT: C 142 MET cc_start: 0.7409 (ppp) cc_final: 0.6796 (ppp) REVERT: C 199 TRP cc_start: 0.4539 (p-90) cc_final: 0.4253 (p-90) REVERT: C 503 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7791 (ttm170) REVERT: C 522 GLU cc_start: 0.7749 (tt0) cc_final: 0.7545 (tt0) REVERT: C 753 GLU cc_start: 0.8059 (mp0) cc_final: 0.7705 (mp0) REVERT: C 999 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7432 (mtm180) REVERT: C 1048 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: D 205 MET cc_start: 0.8828 (mtt) cc_final: 0.8526 (mtt) REVERT: D 229 LEU cc_start: 0.6527 (mt) cc_final: 0.6245 (mt) REVERT: D 312 MET cc_start: 0.8544 (mmt) cc_final: 0.8223 (mmt) REVERT: D 772 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7555 (mm) REVERT: D 803 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7590 (mtm-85) REVERT: D 825 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: D 872 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (mt) REVERT: D 892 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7962 (mp) REVERT: D 1077 ARG cc_start: 0.6913 (ptm-80) cc_final: 0.6494 (ttp80) REVERT: E 12 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7539 (pt) REVERT: E 49 GLU cc_start: 0.2400 (OUTLIER) cc_final: 0.2112 (pm20) REVERT: F 277 HIS cc_start: 0.8648 (m-70) cc_final: 0.8411 (m170) REVERT: F 282 ASN cc_start: 0.8094 (m110) cc_final: 0.7753 (t0) REVERT: F 320 TYR cc_start: 0.7964 (p90) cc_final: 0.7614 (p90) REVERT: F 369 MET cc_start: 0.9224 (ppp) cc_final: 0.9003 (tmm) REVERT: F 386 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8591 (pp) REVERT: F 388 MET cc_start: 0.7713 (mpp) cc_final: 0.7478 (mpp) REVERT: G 38 MET cc_start: 0.4513 (ppp) cc_final: 0.3654 (pmm) REVERT: H 127 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.6135 (t80) REVERT: N 38 MET cc_start: 0.1801 (ptt) cc_final: 0.1301 (ppp) outliers start: 132 outliers final: 89 residues processed: 396 average time/residue: 0.2077 time to fit residues: 137.6082 Evaluate side-chains 379 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 276 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1092 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 803 ARG Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 925 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 391 optimal weight: 50.0000 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 363 optimal weight: 50.0000 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 358 optimal weight: 50.0000 chunk 184 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 488 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.189860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137657 restraints weight = 56851.997| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.65 r_work: 0.3337 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35847 Z= 0.162 Angle : 0.646 11.572 49167 Z= 0.338 Chirality : 0.046 0.367 5581 Planarity : 0.004 0.055 5854 Dihedral : 20.070 175.780 6227 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.55 % Allowed : 22.23 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.13), residues: 4029 helix: 1.36 (0.13), residues: 1684 sheet: -0.18 (0.23), residues: 492 loop : -0.64 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 146 TYR 0.035 0.001 TYR E 32 PHE 0.029 0.002 PHE D 248 TRP 0.055 0.002 TRP D 651 HIS 0.009 0.001 HIS N 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (35779) covalent geometry : angle 0.63436 / 0.34 (49119) hydrogen bonds : bond 0.04103 / 2.81 ( 1655) hydrogen bonds : angle 4.31651 / 3.02 ( 4593) metal coordination : bond 0.00372 / 0.23 ( 68) metal coordination : angle 3.93714 / 2.64 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 281 time to evaluate : 1.315 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: A 76 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 146 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 151 GLN cc_start: 0.7707 (pm20) cc_final: 0.7455 (pm20) REVERT: A 165 ASP cc_start: 0.8610 (p0) cc_final: 0.7062 (p0) REVERT: B 43 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 70 LYS cc_start: 0.8713 (tptt) cc_final: 0.8149 (tptt) REVERT: B 151 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 152 ASN cc_start: 0.7448 (m-40) cc_final: 0.6779 (p0) REVERT: B 208 MET cc_start: 0.7600 (ttm) cc_final: 0.7171 (ttp) REVERT: C 142 MET cc_start: 0.7438 (ppp) cc_final: 0.6816 (ppp) REVERT: C 199 TRP cc_start: 0.4735 (p-90) cc_final: 0.4388 (p-90) REVERT: C 503 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7789 (ttm170) REVERT: C 753 GLU cc_start: 0.8043 (mp0) cc_final: 0.7687 (mp0) REVERT: C 999 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7427 (mtm180) REVERT: C 1048 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: D 205 MET cc_start: 0.8901 (mtt) cc_final: 0.8622 (mtt) REVERT: D 229 LEU cc_start: 0.6594 (mt) cc_final: 0.6316 (mt) REVERT: D 772 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7552 (mm) REVERT: D 803 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7593 (mtm-85) REVERT: D 825 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: D 872 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8859 (mt) REVERT: D 892 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (mp) REVERT: D 1006 MET cc_start: 0.4743 (ttt) cc_final: 0.4451 (ttp) REVERT: D 1077 ARG cc_start: 0.6903 (ptm-80) cc_final: 0.6487 (ttp80) REVERT: E 12 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7547 (pt) REVERT: E 49 GLU cc_start: 0.2396 (OUTLIER) cc_final: 0.2120 (pm20) REVERT: F 277 HIS cc_start: 0.8670 (m-70) cc_final: 0.8449 (m170) REVERT: F 282 ASN cc_start: 0.8117 (m110) cc_final: 0.7733 (t0) REVERT: F 320 TYR cc_start: 0.7930 (p90) cc_final: 0.7585 (p90) REVERT: F 369 MET cc_start: 0.9195 (ppp) cc_final: 0.8943 (tmm) REVERT: F 386 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8551 (pp) REVERT: F 388 MET cc_start: 0.7659 (mpp) cc_final: 0.7438 (mpp) REVERT: H 127 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.6122 (t80) REVERT: N 38 MET cc_start: 0.1833 (ptt) cc_final: 0.1388 (ppp) outliers start: 119 outliers final: 94 residues processed: 379 average time/residue: 0.1977 time to fit residues: 126.2398 Evaluate side-chains 375 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 266 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1013 MET Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 803 ARG Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 314 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 413 optimal weight: 30.0000 chunk 354 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 382 optimal weight: 50.0000 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.188473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135302 restraints weight = 57059.066| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.73 r_work: 0.3316 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35847 Z= 0.200 Angle : 0.676 12.606 49167 Z= 0.351 Chirality : 0.046 0.357 5581 Planarity : 0.004 0.057 5854 Dihedral : 20.087 175.489 6227 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.64 % Allowed : 22.23 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.13), residues: 4029 helix: 1.29 (0.13), residues: 1679 sheet: -0.20 (0.23), residues: 479 loop : -0.69 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 146 TYR 0.035 0.002 TYR E 32 PHE 0.028 0.002 PHE D 248 TRP 0.055 0.002 TRP D 651 HIS 0.007 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (35779) covalent geometry : angle 0.66341 / 0.35 (49119) hydrogen bonds : bond 0.04248 / 2.91 ( 1655) hydrogen bonds : angle 4.38224 / 3.07 ( 4593) metal coordination : bond 0.00413 / 0.25 ( 68) metal coordination : angle 4.19736 / 2.81 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 273 time to evaluate : 1.168 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: symmetry clash REVERT: A 76 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8732 (tt) REVERT: A 146 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 151 GLN cc_start: 0.7709 (pm20) cc_final: 0.7427 (pm20) REVERT: A 165 ASP cc_start: 0.8618 (p0) cc_final: 0.7071 (p0) REVERT: B 43 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (mp) REVERT: B 151 GLN cc_start: 0.8298 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 152 ASN cc_start: 0.7518 (m-40) cc_final: 0.7097 (p0) REVERT: B 208 MET cc_start: 0.7739 (ttm) cc_final: 0.7343 (ttp) REVERT: C 142 MET cc_start: 0.7624 (ppp) cc_final: 0.6996 (ppp) REVERT: C 199 TRP cc_start: 0.4960 (p-90) cc_final: 0.4604 (p-90) REVERT: C 503 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7781 (ttm170) REVERT: C 673 LYS cc_start: 0.8528 (mptt) cc_final: 0.8327 (mppt) REVERT: C 753 GLU cc_start: 0.8111 (mp0) cc_final: 0.7771 (mp0) REVERT: C 999 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7513 (mtm180) REVERT: C 1048 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: D 205 MET cc_start: 0.8876 (mtt) cc_final: 0.8575 (mtt) REVERT: D 229 LEU cc_start: 0.6362 (mt) cc_final: 0.6063 (mt) REVERT: D 803 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: D 825 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: D 872 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8940 (mm) REVERT: D 892 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (mp) REVERT: D 919 MET cc_start: 0.8099 (mmm) cc_final: 0.7362 (mmm) REVERT: D 1006 MET cc_start: 0.4682 (ttt) cc_final: 0.4344 (ttp) REVERT: D 1077 ARG cc_start: 0.7025 (ptm-80) cc_final: 0.6579 (ttp80) REVERT: E 12 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7604 (pt) REVERT: E 49 GLU cc_start: 0.2457 (OUTLIER) cc_final: 0.2176 (pm20) REVERT: F 238 LYS cc_start: 0.9098 (mttp) cc_final: 0.8813 (mmtm) REVERT: F 277 HIS cc_start: 0.8684 (m-70) cc_final: 0.8431 (m170) REVERT: F 282 ASN cc_start: 0.8131 (m110) cc_final: 0.7721 (t0) REVERT: G 38 MET cc_start: 0.4489 (ppp) cc_final: 0.3533 (pmm) REVERT: H 127 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.6147 (t80) REVERT: N 38 MET cc_start: 0.1552 (ptt) cc_final: 0.1104 (ppp) outliers start: 122 outliers final: 101 residues processed: 376 average time/residue: 0.1969 time to fit residues: 123.7470 Evaluate side-chains 377 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 263 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1013 MET Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 742 LYS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 803 ARG Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1036 LYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1211 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 238 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 315 optimal weight: 8.9990 chunk 300 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 chunk 226 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 385 optimal weight: 10.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN D 213 GLN D 329 GLN D 579 GLN F 488 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.190354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136703 restraints weight = 56720.463| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.77 r_work: 0.3357 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 35847 Z= 0.139 Angle : 0.646 11.510 49167 Z= 0.338 Chirality : 0.045 0.473 5581 Planarity : 0.004 0.053 5854 Dihedral : 20.070 175.932 6225 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.04 % Allowed : 22.88 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4029 helix: 1.42 (0.13), residues: 1678 sheet: -0.14 (0.23), residues: 484 loop : -0.64 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 146 TYR 0.035 0.001 TYR E 32 PHE 0.036 0.002 PHE C 127 TRP 0.050 0.002 TRP D 651 HIS 0.006 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (35779) covalent geometry : angle 0.63631 / 0.34 (49119) hydrogen bonds : bond 0.03944 / 2.70 ( 1655) hydrogen bonds : angle 4.30096 / 3.01 ( 4593) metal coordination : bond 0.00330 / 0.22 ( 68) metal coordination : angle 3.62782 / 2.43 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9904.71 seconds wall clock time: 169 minutes 52.38 seconds (10192.38 seconds total)