Starting phenix.real_space_refine on Sun Jul 28 08:23:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s51_19718/07_2024/8s51_19718_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 10 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 27878 2.51 5 N 7882 2.21 5 O 8651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 44796 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11257 Classifications: {'peptide': 1421} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8971 Classifications: {'peptide': 1121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 4 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2252 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 14, 'TRANS': 277} Chain breaks: 1 Chain: "N" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1113 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "P" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1270 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 72.079 107.492 86.117 1.00 56.68 S ATOM 486 SG CYS A 74 68.475 106.610 86.638 1.00 53.79 S ATOM 533 SG CYS A 81 71.139 104.057 87.066 1.00 55.14 S ATOM 768 SG CYS A 111 71.360 75.671 49.751 1.00 73.10 S ATOM 796 SG CYS A 114 67.418 76.654 48.815 1.00 82.58 S ATOM 1109 SG CYS A 154 69.140 73.246 48.477 1.00 94.09 S ATOM 1132 SG CYS A 184 69.658 76.442 46.248 1.00 93.57 S ATOM 19797 SG CYS B1119 57.603 96.306 78.738 1.00 45.39 S ATOM 19819 SG CYS B1122 60.796 94.773 77.331 1.00 47.41 S ATOM 19934 SG CYS B1137 60.517 98.542 77.750 1.00 58.00 S ATOM 19955 SG CYS B1140 58.667 96.535 75.007 1.00 63.60 S ATOM 20922 SG CYS C 88 88.216 108.359 151.949 1.00 55.93 S ATOM 20935 SG CYS C 90 89.702 109.981 148.874 1.00 62.04 S ATOM 20970 SG CYS C 94 91.613 109.970 152.142 1.00 48.02 S ATOM 20992 SG CYS C 97 91.310 106.786 150.224 1.00 45.38 S ATOM 28278 SG CYS I 17 125.824 44.533 53.436 1.00 74.02 S ATOM 28302 SG CYS I 20 124.448 48.121 53.282 1.00 71.80 S ATOM 28463 SG CYS I 39 122.000 45.320 53.396 1.00 73.19 S ATOM 28488 SG CYS I 42 124.212 45.871 50.332 1.00 80.79 S ATOM 28840 SG CYS I 86 133.322 29.727 94.890 1.00 55.15 S ATOM 28864 SG CYS I 89 137.152 30.934 95.594 1.00 61.48 S ATOM 29068 SG CYS I 114 134.035 33.131 95.964 1.00 41.59 S ATOM 29103 SG CYS I 119 135.378 32.078 92.619 1.00 53.71 S ATOM 29214 SG CYS J 7 105.929 80.007 142.546 1.00 13.78 S ATOM 29238 SG CYS J 10 104.304 79.639 145.987 1.00 15.01 S ATOM 29502 SG CYS J 44 105.298 76.510 144.218 1.00 18.07 S ATOM 29508 SG CYS J 45 107.801 78.914 145.724 1.00 18.24 S ATOM 30628 SG CYS L 19 120.099 111.951 116.535 1.00 40.03 S ATOM 30647 SG CYS L 22 122.181 113.818 119.074 1.00 47.87 S ATOM 30764 SG CYS L 36 121.006 115.590 115.961 1.00 53.06 S ATOM 30790 SG CYS L 39 123.676 112.856 115.722 1.00 54.29 S ATOM 30972 SG CYS M 15 68.120 116.728 109.118 1.00 80.12 S ATOM 31119 SG CYS M 34 70.740 114.929 111.058 1.00 69.39 S ATOM 31141 SG CYS M 37 67.492 115.568 112.747 1.00 73.44 S ATOM 42845 SG CYS W 129 61.136 131.794 78.164 1.00471.42 S ATOM 43037 SG CYS W 154 61.380 129.738 82.002 1.00440.30 S ATOM 43061 SG CYS W 157 62.999 132.450 81.096 1.00451.85 S Time building chain proxies: 24.84, per 1000 atoms: 0.55 Number of scatterers: 44796 At special positions: 0 Unit cell: (179.55, 176.4, 185.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 250 16.00 P 124 15.00 Mg 1 11.99 O 8651 8.00 N 7882 7.00 C 27878 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 - 3.50 Amino acid : False - 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: 18.87 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " Number of angles added : 48 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9950 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 54 sheets defined 39.9% alpha, 15.9% beta 54 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 17.46 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.598A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.644A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.772A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.518A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.584A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.748A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.589A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.673A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.059A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.641A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.860A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.550A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 867 removed outlier: 3.764A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.924A pdb=" N SER A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 901' Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.620A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.516A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.913A pdb=" N TRP A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1200 through 1204 removed outlier: 3.787A pdb=" N VAL A1204 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1293 removed outlier: 4.146A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 removed outlier: 3.907A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1387 removed outlier: 3.610A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.596A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.819A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1466 through 1469 removed outlier: 3.705A pdb=" N GLY A1469 " --> pdb=" O ALA A1466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1466 through 1469' Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.675A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.712A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.504A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.711A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.526A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.904A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.325A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.743A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.595A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.547A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 969 through 972 removed outlier: 3.616A pdb=" N ILE B 972 " --> pdb=" O PRO B 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 969 through 972' Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.589A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.639A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.657A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.580A pdb=" N HIS C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.701A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.519A pdb=" N TRP C 176 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 270 removed outlier: 3.634A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.871A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 4.121A pdb=" N MET D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.737A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.700A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.717A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.046A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 119 removed outlier: 4.073A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.637A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.925A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.158A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 4.265A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.511A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.812A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.096A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'M' and resid 89 through 91 No H-bonds generated for 'chain 'M' and resid 89 through 91' Processing helix chain 'M' and resid 108 through 128 removed outlier: 3.505A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.557A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.797A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'M' and resid 225 through 243 Processing helix chain 'M' and resid 249 through 264 removed outlier: 3.575A pdb=" N VAL M 253 " --> pdb=" O SER M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 283 through 293 removed outlier: 4.381A pdb=" N LEU M 291 " --> pdb=" O GLN M 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.718A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'O' and resid 179 through 186 Processing helix chain 'O' and resid 226 through 244 removed outlier: 3.617A pdb=" N LEU O 244 " --> pdb=" O VAL O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 277 removed outlier: 3.651A pdb=" N LEU O 273 " --> pdb=" O ARG O 269 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU O 275 " --> pdb=" O GLU O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 335 removed outlier: 4.030A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix removed outlier: 3.648A pdb=" N PHE O 335 " --> pdb=" O ILE O 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.747A pdb=" N LYS Q 36 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 164 removed outlier: 3.581A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 180 removed outlier: 4.000A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 24 through 35 removed outlier: 3.521A pdb=" N SER R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.684A pdb=" N ASN R 64 " --> pdb=" O GLU R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 136 Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 194 removed outlier: 3.656A pdb=" N ASP R 185 " --> pdb=" O GLN R 181 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET R 186 " --> pdb=" O HIS R 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 203 removed outlier: 3.844A pdb=" N VAL R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.730A pdb=" N LYS R 218 " --> pdb=" O LYS R 214 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU R 219 " --> pdb=" O GLU R 215 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.696A pdb=" N ASP U 32 " --> pdb=" O ILE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 51 removed outlier: 4.060A pdb=" N MET U 40 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU U 50 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 330 removed outlier: 3.945A pdb=" N ASP U 330 " --> pdb=" O GLN U 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 51 Processing helix chain 'W' and resid 11 through 23 removed outlier: 3.831A pdb=" N LYS W 15 " --> pdb=" O PRO W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 40 Processing helix chain 'W' and resid 45 through 53 removed outlier: 3.591A pdb=" N LEU W 52 " --> pdb=" O MET W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 70 removed outlier: 3.558A pdb=" N VAL W 62 " --> pdb=" O GLN W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 124 removed outlier: 3.826A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 145 removed outlier: 4.043A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 166 removed outlier: 3.585A pdb=" N SER W 166 " --> pdb=" O GLU W 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 163 through 166' Processing helix chain 'W' and resid 167 through 184 removed outlier: 3.893A pdb=" N LYS W 171 " --> pdb=" O ALA W 167 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE W 184 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 194 Processing helix chain 'X' and resid 76 through 91 removed outlier: 4.067A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 106 removed outlier: 4.266A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR X 106 " --> pdb=" O ILE X 102 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing helix chain 'X' and resid 122 through 127 removed outlier: 3.697A pdb=" N ASN X 127 " --> pdb=" O ALA X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 161 Processing helix chain 'X' and resid 168 through 175 Processing helix chain 'X' and resid 177 through 186 removed outlier: 4.337A pdb=" N ALA X 181 " --> pdb=" O ASN X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 223 removed outlier: 3.597A pdb=" N VAL X 223 " --> pdb=" O LEU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 241 removed outlier: 3.978A pdb=" N ILE X 233 " --> pdb=" O ASP X 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.601A pdb=" N SER A 194 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.936A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.009A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG A 426 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET M 32 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 7.043A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.554A pdb=" N GLY A 789 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.888A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.928A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.597A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB8, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.835A pdb=" N ILE B 65 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.481A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 216 removed outlier: 3.789A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 633 current: chain 'B' and resid 695 through 696 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.459A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 808 through 817 current: chain 'B' and resid 902 through 911 removed outlier: 6.961A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 917 through 927 current: chain 'L' and resid 44 through 46 Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.313A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD3, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD4, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1127 through 1129 removed outlier: 3.555A pdb=" N ASN B1129 " --> pdb=" O THR B1134 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B1134 " --> pdb=" O ASN B1129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.740A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.643A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.652A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.581A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 104 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.699A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.745A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG G 151 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 158 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE5, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.939A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU H 31 " --> pdb=" O ASP H 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE H 6 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 93 through 94 removed outlier: 3.690A pdb=" N ASN M 98 " --> pdb=" O ASP M 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 200 through 203 removed outlier: 3.757A pdb=" N VAL O 200 " --> pdb=" O ILE O 213 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE O 213 " --> pdb=" O VAL O 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET O 202 " --> pdb=" O ALA O 211 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER O 170 " --> pdb=" O CYS O 221 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN O 164 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL O 259 " --> pdb=" O GLN O 166 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE O 168 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN O 257 " --> pdb=" O ILE O 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER O 170 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE O 255 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL O 172 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE O 253 " --> pdb=" O VAL O 172 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE O 300 " --> pdb=" O MET O 295 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE O 292 " --> pdb=" O SER O 282 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 191 through 192 removed outlier: 3.507A pdb=" N TYR O 192 " --> pdb=" O PHE V 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'Q' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 12 current: chain 'Q' and resid 98 through 102 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 114 current: chain 'Q' and resid 135 through 139 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 135 through 139 current: chain 'R' and resid 52 through 58 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 82 current: chain 'R' and resid 104 through 115 Processing sheet with id=AF4, first strand: chain 'R' and resid 223 through 224 removed outlier: 3.868A pdb=" N ASN R 224 " --> pdb=" O THR R 232 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR R 232 " --> pdb=" O ASN R 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'U' and resid 363 through 367 removed outlier: 3.882A pdb=" N TYR U 365 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET U 358 " --> pdb=" O TYR U 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE U 367 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN U 359 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL U 334 " --> pdb=" O ASN U 359 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN U 333 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL V 96 " --> pdb=" O ASN U 333 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N CYS V 98 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS U 337 " --> pdb=" O CYS V 98 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL V 75 " --> pdb=" O ASN V 63 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL V 79 " --> pdb=" O ARG V 59 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG V 59 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE V 81 " --> pdb=" O ASN V 57 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN V 57 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS U 369 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE V 58 " --> pdb=" O LYS U 369 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE U 371 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY V 60 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP U 373 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU V 62 " --> pdb=" O ASP U 373 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU U 375 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR V 64 " --> pdb=" O GLU U 375 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY U 372 " --> pdb=" O PHE U 351 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE U 351 " --> pdb=" O GLY U 372 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA U 374 " --> pdb=" O TRP U 349 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 42 through 44 removed outlier: 3.555A pdb=" N TYR W 92 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU W 79 " --> pdb=" O THR W 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS W 89 " --> pdb=" O ARG W 77 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG W 77 " --> pdb=" O HIS W 89 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.557A pdb=" N PHE W 127 " --> pdb=" O PHE W 136 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 130 through 133 Processing sheet with id=AF9, first strand: chain 'X' and resid 166 through 167 removed outlier: 3.527A pdb=" N ILE X 166 " --> pdb=" O LEU X 201 " (cutoff:3.500A) 1654 hydrogen bonds defined for protein. 4707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 27.25 Time building geometry restraints manager: 20.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12242 1.33 - 1.46: 9099 1.46 - 1.58: 23893 1.58 - 1.70: 242 1.70 - 1.83: 394 Bond restraints: 45870 Sorted by residual: bond pdb=" CB GLN A 461 " pdb=" CG GLN A 461 " ideal model delta sigma weight residual 1.520 1.386 0.134 3.00e-02 1.11e+03 1.99e+01 bond pdb=" N SER M 65 " pdb=" CA SER M 65 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.90e-02 2.77e+03 7.38e+00 bond pdb=" N ILE A1486 " pdb=" CA ILE A1486 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.20e-02 6.94e+03 7.31e+00 bond pdb=" N ASP E 46 " pdb=" CA ASP E 46 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.40e-02 5.10e+03 6.23e+00 bond pdb=" N GLY A 183 " pdb=" CA GLY A 183 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.08e-02 8.57e+03 6.22e+00 ... (remaining 45865 not shown) Histogram of bond angle deviations from ideal: 96.48 - 104.03: 890 104.03 - 111.58: 20345 111.58 - 119.13: 17563 119.13 - 126.69: 22838 126.69 - 134.24: 819 Bond angle restraints: 62455 Sorted by residual: angle pdb=" C GLU E 97 " pdb=" N ASN E 98 " pdb=" CA ASN E 98 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA GLN M 148 " pdb=" CB GLN M 148 " pdb=" CG GLN M 148 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" O5' DC N 57 " pdb=" C5' DC N 57 " pdb=" C4' DC N 57 " ideal model delta sigma weight residual 110.80 117.21 -6.41 1.50e+00 4.44e-01 1.82e+01 angle pdb=" CB MET M 215 " pdb=" CG MET M 215 " pdb=" SD MET M 215 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C2' DT T 41 " pdb=" C1' DT T 41 " pdb=" N1 DT T 41 " ideal model delta sigma weight residual 113.50 119.67 -6.17 1.50e+00 4.44e-01 1.69e+01 ... (remaining 62450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.33: 26013 27.33 - 54.66: 1551 54.66 - 81.99: 192 81.99 - 109.33: 22 109.33 - 136.66: 1 Dihedral angle restraints: 27779 sinusoidal: 12419 harmonic: 15360 Sorted by residual: dihedral pdb=" CA ILE Q 28 " pdb=" C ILE Q 28 " pdb=" N MET Q 29 " pdb=" CA MET Q 29 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ARG A 460 " pdb=" C ARG A 460 " pdb=" N GLN A 461 " pdb=" CA GLN A 461 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLY A 498 " pdb=" C GLY A 498 " pdb=" N ASP A 499 " pdb=" CA ASP A 499 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 27776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 6740 0.132 - 0.264: 172 0.264 - 0.396: 6 0.396 - 0.528: 28 0.528 - 0.659: 28 Chirality restraints: 6974 Sorted by residual: chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DG N 30 " pdb=" OP1 DG N 30 " pdb=" OP2 DG N 30 " pdb=" O5' DG N 30 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC T 69 " pdb=" OP1 DC T 69 " pdb=" OP2 DC T 69 " pdb=" O5' DC T 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 6971 not shown) Planarity restraints: 7662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT T 34 " -0.117 2.00e-02 2.50e+03 5.41e-02 7.31e+01 pdb=" N1 DT T 34 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT T 34 " 0.052 2.00e-02 2.50e+03 pdb=" O2 DT T 34 " 0.040 2.00e-02 2.50e+03 pdb=" N3 DT T 34 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT T 34 " -0.014 2.00e-02 2.50e+03 pdb=" O4 DT T 34 " -0.086 2.00e-02 2.50e+03 pdb=" C5 DT T 34 " 0.023 2.00e-02 2.50e+03 pdb=" C7 DT T 34 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DT T 34 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 41 " -0.090 2.00e-02 2.50e+03 4.60e-02 5.30e+01 pdb=" N1 DT T 41 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DT T 41 " 0.035 2.00e-02 2.50e+03 pdb=" O2 DT T 41 " 0.061 2.00e-02 2.50e+03 pdb=" N3 DT T 41 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT T 41 " -0.016 2.00e-02 2.50e+03 pdb=" O4 DT T 41 " -0.072 2.00e-02 2.50e+03 pdb=" C5 DT T 41 " 0.018 2.00e-02 2.50e+03 pdb=" C7 DT T 41 " 0.046 2.00e-02 2.50e+03 pdb=" C6 DT T 41 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 35 " -0.100 2.00e-02 2.50e+03 4.62e-02 4.80e+01 pdb=" N1 DC T 35 " 0.044 2.00e-02 2.50e+03 pdb=" C2 DC T 35 " 0.017 2.00e-02 2.50e+03 pdb=" O2 DC T 35 " 0.035 2.00e-02 2.50e+03 pdb=" N3 DC T 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC T 35 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC T 35 " -0.055 2.00e-02 2.50e+03 pdb=" C5 DC T 35 " 0.028 2.00e-02 2.50e+03 pdb=" C6 DC T 35 " 0.044 2.00e-02 2.50e+03 ... (remaining 7659 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 151 2.49 - 3.09: 28463 3.09 - 3.69: 68183 3.69 - 4.30: 97952 4.30 - 4.90: 161235 Nonbonded interactions: 355984 Sorted by model distance: nonbonded pdb=" OP1 G P 8 " pdb="MG MG A2003 " model vdw 1.887 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.898 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.953 2.170 nonbonded pdb=" O3' A P 7 " pdb="MG MG A2003 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 2.084 2.170 ... (remaining 355979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.850 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 149.870 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.200 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 45870 Z= 0.520 Angle : 0.870 12.566 62455 Z= 0.459 Chirality : 0.075 0.659 6974 Planarity : 0.007 0.124 7662 Dihedral : 16.318 136.656 17829 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 0.17 % Allowed : 0.41 % Favored : 99.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.10), residues: 5206 helix: -2.47 (0.08), residues: 1850 sheet: 0.12 (0.20), residues: 713 loop : -0.98 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 52 HIS 0.020 0.001 HIS B 481 PHE 0.048 0.002 PHE A1432 TYR 0.038 0.002 TYR B 766 ARG 0.017 0.001 ARG M 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 708 time to evaluate : 5.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 GLN cc_start: 0.7768 (tp40) cc_final: 0.7541 (tp40) REVERT: A 1433 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5787 (mt-10) REVERT: B 555 GLU cc_start: 0.6716 (tp30) cc_final: 0.6463 (tp30) REVERT: M 258 ILE cc_start: 0.8403 (mm) cc_final: 0.8166 (mm) REVERT: W 48 MET cc_start: 0.8676 (ppp) cc_final: 0.8376 (ppp) outliers start: 8 outliers final: 0 residues processed: 713 average time/residue: 0.5923 time to fit residues: 701.9258 Evaluate side-chains 595 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 594 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 413 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 251 optimal weight: 2.9990 chunk 308 optimal weight: 0.0020 chunk 479 optimal weight: 3.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN A 273 GLN A 341 GLN A 461 GLN A 531 ASN A 601 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 791 GLN A1005 HIS A1042 ASN A1077 ASN A1105 ASN A1417 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 683 GLN B 717 ASN B 980 HIS B1068 GLN B1071 ASN B1101 GLN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 111 GLN C 260 GLN D 19 GLN E 30 GLN E 168 ASN G 4 HIS H 29 HIS H 87 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN K 29 ASN K 89 ASN K 113 GLN M 102 GLN O 277 HIS ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 HIS W 58 GLN X 83 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45870 Z= 0.189 Angle : 0.549 11.191 62455 Z= 0.293 Chirality : 0.042 0.237 6974 Planarity : 0.004 0.067 7662 Dihedral : 13.652 128.490 7112 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 7.37 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5206 helix: -0.05 (0.11), residues: 1909 sheet: 0.15 (0.19), residues: 738 loop : -0.73 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.006 0.001 HIS D 93 PHE 0.014 0.001 PHE A1388 TYR 0.026 0.001 TYR I 44 ARG 0.005 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 655 time to evaluate : 5.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6862 (ttp80) REVERT: A 499 ASP cc_start: 0.7490 (m-30) cc_final: 0.7086 (m-30) REVERT: A 1433 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6264 (mt-10) REVERT: B 555 GLU cc_start: 0.6656 (tp30) cc_final: 0.6411 (tp30) REVERT: O 219 MET cc_start: 0.6940 (tpt) cc_final: 0.6684 (tpt) outliers start: 40 outliers final: 22 residues processed: 677 average time/residue: 0.5570 time to fit residues: 632.3609 Evaluate side-chains 615 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 592 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 chunk 326 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 480 optimal weight: 0.5980 chunk 518 optimal weight: 50.0000 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 10.0000 chunk 163 optimal weight: 0.0370 chunk 385 optimal weight: 0.0010 overall best weight: 0.6866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 168 ASN H 29 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN K 29 ASN M 102 GLN O 229 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45870 Z= 0.196 Angle : 0.514 13.769 62455 Z= 0.271 Chirality : 0.041 0.190 6974 Planarity : 0.004 0.059 7662 Dihedral : 13.652 130.937 7112 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.22 % Allowed : 10.52 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 5206 helix: 0.79 (0.12), residues: 1906 sheet: 0.23 (0.20), residues: 728 loop : -0.63 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS M 18 PHE 0.022 0.001 PHE O 280 TYR 0.023 0.001 TYR B 766 ARG 0.005 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 631 time to evaluate : 5.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 190 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6796 (ttp80) REVERT: A 234 PHE cc_start: 0.7904 (t80) cc_final: 0.7624 (t80) REVERT: A 499 ASP cc_start: 0.7400 (m-30) cc_final: 0.7008 (m-30) REVERT: B 555 GLU cc_start: 0.6602 (tp30) cc_final: 0.6363 (tp30) REVERT: I 16 PHE cc_start: 0.8590 (m-80) cc_final: 0.8380 (m-80) REVERT: M 215 MET cc_start: 0.7525 (mmm) cc_final: 0.7275 (mmm) outliers start: 57 outliers final: 34 residues processed: 657 average time/residue: 0.5600 time to fit residues: 615.4373 Evaluate side-chains 627 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 593 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 282 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 30.0000 chunk 361 optimal weight: 0.0270 chunk 249 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 482 optimal weight: 40.0000 chunk 510 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 456 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 790 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 537 GLN B 593 GLN B1097 HIS C 66 HIS C 83 GLN C 111 GLN C 217 GLN E 98 ASN H 29 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN M 102 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 GLN W 58 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 45870 Z= 0.425 Angle : 0.617 14.641 62455 Z= 0.320 Chirality : 0.045 0.214 6974 Planarity : 0.004 0.055 7662 Dihedral : 13.811 132.067 7112 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.76 % Allowed : 12.13 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5206 helix: 0.99 (0.12), residues: 1899 sheet: 0.04 (0.19), residues: 738 loop : -0.69 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 49 HIS 0.007 0.001 HIS B 387 PHE 0.024 0.002 PHE O 214 TYR 0.028 0.002 TYR B 766 ARG 0.008 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 640 time to evaluate : 5.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7023 (ttp80) cc_final: 0.6772 (ttp80) REVERT: A 438 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6707 (mp) REVERT: A 499 ASP cc_start: 0.7510 (m-30) cc_final: 0.7255 (m-30) REVERT: A 1307 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 1423 ASP cc_start: 0.7139 (t0) cc_final: 0.6686 (t0) REVERT: B 343 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 529 MET cc_start: 0.7928 (mtp) cc_final: 0.7693 (mmm) REVERT: F 94 MET cc_start: 0.7336 (tpp) cc_final: 0.7028 (mtt) REVERT: H 35 PHE cc_start: 0.7940 (m-10) cc_final: 0.7710 (m-10) REVERT: K 81 TYR cc_start: 0.7446 (t80) cc_final: 0.7223 (t80) REVERT: L 47 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7810 (mtpt) REVERT: O 253 PHE cc_start: 0.6471 (t80) cc_final: 0.6268 (t80) outliers start: 82 outliers final: 53 residues processed: 674 average time/residue: 0.5641 time to fit residues: 636.3054 Evaluate side-chains 655 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 599 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 924 TYR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 380 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 435 optimal weight: 0.0970 chunk 352 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 458 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B1101 GLN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN O 229 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 45870 Z= 0.267 Angle : 0.545 14.037 62455 Z= 0.283 Chirality : 0.042 0.186 6974 Planarity : 0.004 0.051 7662 Dihedral : 13.802 131.353 7112 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 14.08 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 5206 helix: 1.23 (0.12), residues: 1887 sheet: 0.04 (0.19), residues: 735 loop : -0.59 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.004 0.001 HIS A 809 PHE 0.027 0.001 PHE O 214 TYR 0.020 0.001 TYR B 84 ARG 0.007 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 633 time to evaluate : 4.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ASP cc_start: 0.7519 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1078 GLN cc_start: 0.8115 (tt0) cc_final: 0.7882 (tt0) REVERT: A 1307 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8458 (p) REVERT: A 1392 TYR cc_start: 0.7869 (t80) cc_final: 0.7326 (t80) REVERT: A 1423 ASP cc_start: 0.7213 (t0) cc_final: 0.6607 (t0) REVERT: B 343 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 529 MET cc_start: 0.7885 (mtp) cc_final: 0.7641 (mmm) REVERT: E 155 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: F 94 MET cc_start: 0.7327 (tpp) cc_final: 0.7031 (mtt) REVERT: L 47 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7795 (mtpt) outliers start: 76 outliers final: 51 residues processed: 665 average time/residue: 0.5720 time to fit residues: 634.7290 Evaluate side-chains 656 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 602 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.0010 chunk 459 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 510 optimal weight: 40.0000 chunk 424 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS C 111 GLN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 29 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 45870 Z= 0.185 Angle : 0.513 12.353 62455 Z= 0.266 Chirality : 0.041 0.207 6974 Planarity : 0.003 0.049 7662 Dihedral : 13.754 131.778 7112 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.69 % Allowed : 14.70 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 5206 helix: 1.46 (0.12), residues: 1894 sheet: 0.13 (0.19), residues: 742 loop : -0.53 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS B1060 PHE 0.024 0.001 PHE O 214 TYR 0.015 0.001 TYR B 766 ARG 0.007 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 633 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6683 (mp) REVERT: A 499 ASP cc_start: 0.7448 (m-30) cc_final: 0.7088 (m-30) REVERT: A 501 MET cc_start: 0.7818 (mtp) cc_final: 0.7594 (mtp) REVERT: A 958 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.7231 (ttp-170) REVERT: A 986 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7186 (mtp) REVERT: A 1392 TYR cc_start: 0.7786 (t80) cc_final: 0.7152 (t80) REVERT: B 343 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8249 (mp) REVERT: E 18 MET cc_start: 0.8371 (mmm) cc_final: 0.8116 (mmm) REVERT: F 94 MET cc_start: 0.7321 (tpp) cc_final: 0.7051 (mtt) REVERT: H 102 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: L 47 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7785 (mtpt) REVERT: O 253 PHE cc_start: 0.6255 (t80) cc_final: 0.5890 (t80) REVERT: W 48 MET cc_start: 0.9017 (tmm) cc_final: 0.8103 (ppp) outliers start: 79 outliers final: 51 residues processed: 668 average time/residue: 0.5776 time to fit residues: 644.1341 Evaluate side-chains 656 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 601 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 373 optimal weight: 0.8980 chunk 289 optimal weight: 20.0000 chunk 430 optimal weight: 7.9990 chunk 285 optimal weight: 20.0000 chunk 508 optimal weight: 0.0970 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 0.3980 chunk 234 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 98 ASN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 45870 Z= 0.226 Angle : 0.536 14.598 62455 Z= 0.273 Chirality : 0.042 0.232 6974 Planarity : 0.003 0.061 7662 Dihedral : 13.767 132.551 7112 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 15.04 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 5206 helix: 1.50 (0.12), residues: 1902 sheet: 0.13 (0.19), residues: 747 loop : -0.53 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.003 0.001 HIS A 809 PHE 0.020 0.001 PHE A1388 TYR 0.028 0.001 TYR I 44 ARG 0.006 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 611 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6695 (mp) REVERT: A 499 ASP cc_start: 0.7448 (m-30) cc_final: 0.7089 (m-30) REVERT: A 501 MET cc_start: 0.7815 (mtp) cc_final: 0.7607 (mtp) REVERT: A 958 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.7254 (ttp-170) REVERT: A 986 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7246 (mtp) REVERT: A 1279 MET cc_start: 0.8208 (tmm) cc_final: 0.7881 (ttm) REVERT: A 1392 TYR cc_start: 0.7835 (t80) cc_final: 0.7215 (t80) REVERT: B 343 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8306 (mp) REVERT: F 94 MET cc_start: 0.7326 (tpp) cc_final: 0.7046 (mtt) REVERT: H 102 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: L 47 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7784 (mtpt) REVERT: O 253 PHE cc_start: 0.6130 (t80) cc_final: 0.5819 (t80) REVERT: W 48 MET cc_start: 0.9030 (tmm) cc_final: 0.8160 (ppp) outliers start: 82 outliers final: 63 residues processed: 650 average time/residue: 0.5724 time to fit residues: 619.8984 Evaluate side-chains 663 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 596 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.0470 chunk 203 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 251 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 111 GLN E 98 ASN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN L 26 ASN O 229 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 45870 Z= 0.210 Angle : 0.532 13.899 62455 Z= 0.271 Chirality : 0.042 0.322 6974 Planarity : 0.003 0.051 7662 Dihedral : 13.791 132.656 7112 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.71 % Allowed : 15.53 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.12), residues: 5206 helix: 1.53 (0.12), residues: 1911 sheet: 0.10 (0.19), residues: 737 loop : -0.51 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.005 0.001 HIS A 432 PHE 0.025 0.001 PHE O 214 TYR 0.014 0.001 TYR B 766 ARG 0.008 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 607 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6698 (mp) REVERT: A 958 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.7240 (ttp-170) REVERT: A 1392 TYR cc_start: 0.7828 (t80) cc_final: 0.7202 (t80) REVERT: B 343 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8328 (mp) REVERT: B 432 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: F 94 MET cc_start: 0.7358 (tpp) cc_final: 0.7079 (mtt) REVERT: H 102 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: L 47 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7778 (mtpt) REVERT: M 102 GLN cc_start: 0.8243 (mm110) cc_final: 0.7993 (mm110) REVERT: O 253 PHE cc_start: 0.6175 (t80) cc_final: 0.5887 (t80) REVERT: V 1 MET cc_start: 0.0026 (tpp) cc_final: -0.0873 (tpp) REVERT: W 48 MET cc_start: 0.9036 (tmm) cc_final: 0.8215 (ppp) REVERT: X 100 ASP cc_start: 0.6650 (m-30) cc_final: 0.6432 (m-30) outliers start: 80 outliers final: 66 residues processed: 645 average time/residue: 0.5841 time to fit residues: 631.7223 Evaluate side-chains 657 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 587 time to evaluate : 4.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 6.9990 chunk 487 optimal weight: 20.0000 chunk 444 optimal weight: 6.9990 chunk 474 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 206 optimal weight: 0.0970 chunk 372 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 chunk 448 optimal weight: 20.0000 chunk 472 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 111 GLN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 45870 Z= 0.457 Angle : 0.645 13.978 62455 Z= 0.328 Chirality : 0.046 0.350 6974 Planarity : 0.004 0.053 7662 Dihedral : 13.965 133.689 7112 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.74 % Allowed : 15.58 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 5206 helix: 1.33 (0.12), residues: 1909 sheet: -0.02 (0.19), residues: 767 loop : -0.62 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 203 HIS 0.008 0.001 HIS B 387 PHE 0.025 0.002 PHE A1388 TYR 0.020 0.002 TYR B 206 ARG 0.008 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 596 time to evaluate : 5.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6864 (mp) REVERT: A 958 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7341 (ttp-170) REVERT: B 343 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 432 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: F 94 MET cc_start: 0.7401 (tpp) cc_final: 0.7085 (mtt) REVERT: H 35 PHE cc_start: 0.7964 (m-10) cc_final: 0.7642 (m-10) REVERT: H 102 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: L 47 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7794 (mtpt) REVERT: M 102 GLN cc_start: 0.8267 (mm110) cc_final: 0.7915 (mm-40) REVERT: V 1 MET cc_start: 0.0052 (tpp) cc_final: -0.0741 (tpp) REVERT: W 48 MET cc_start: 0.9064 (tmm) cc_final: 0.8235 (ppp) outliers start: 81 outliers final: 65 residues processed: 633 average time/residue: 0.5766 time to fit residues: 604.0931 Evaluate side-chains 650 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 581 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.0670 chunk 501 optimal weight: 9.9990 chunk 306 optimal weight: 0.8980 chunk 237 optimal weight: 0.5980 chunk 348 optimal weight: 0.9980 chunk 526 optimal weight: 0.9990 chunk 484 optimal weight: 50.0000 chunk 418 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 323 optimal weight: 0.9980 chunk 256 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1236 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 111 GLN E 98 ASN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45870 Z= 0.187 Angle : 0.549 13.841 62455 Z= 0.279 Chirality : 0.042 0.352 6974 Planarity : 0.003 0.057 7662 Dihedral : 13.910 132.452 7112 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.33 % Allowed : 16.24 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 5206 helix: 1.55 (0.12), residues: 1900 sheet: 0.01 (0.19), residues: 740 loop : -0.51 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 203 HIS 0.005 0.001 HIS A 432 PHE 0.024 0.001 PHE A1388 TYR 0.026 0.001 TYR I 44 ARG 0.010 0.000 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10412 Ramachandran restraints generated. 5206 Oldfield, 0 Emsley, 5206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 605 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6809 (mp) REVERT: A 958 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.7232 (ttp-170) REVERT: A 1392 TYR cc_start: 0.7808 (t80) cc_final: 0.7164 (t80) REVERT: B 343 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8315 (mp) REVERT: B 432 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: D 88 LEU cc_start: 0.7764 (mm) cc_final: 0.7552 (pt) REVERT: E 18 MET cc_start: 0.8440 (mmm) cc_final: 0.8198 (mmm) REVERT: E 34 ASP cc_start: 0.8186 (m-30) cc_final: 0.7875 (m-30) REVERT: F 94 MET cc_start: 0.7345 (tpp) cc_final: 0.7061 (mtt) REVERT: H 35 PHE cc_start: 0.7936 (m-10) cc_final: 0.7673 (m-10) REVERT: L 47 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7779 (mtpt) REVERT: M 102 GLN cc_start: 0.8248 (mm110) cc_final: 0.8003 (mm110) REVERT: O 253 PHE cc_start: 0.6172 (t80) cc_final: 0.5916 (t80) REVERT: W 48 MET cc_start: 0.9050 (tmm) cc_final: 0.8232 (ppp) outliers start: 62 outliers final: 53 residues processed: 631 average time/residue: 0.5815 time to fit residues: 608.1146 Evaluate side-chains 638 residues out of total 4667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 582 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 THR Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 20.0000 chunk 446 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 386 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 430 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 98 ASN H 131 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 229 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.190117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101936 restraints weight = 54350.092| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.09 r_work: 0.2938 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 45870 Z= 0.236 Angle : 0.633 59.199 62455 Z= 0.340 Chirality : 0.043 0.567 6974 Planarity : 0.004 0.056 7662 Dihedral : 13.920 132.448 7112 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 16.18 % Favored : 82.47 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5206 helix: 1.55 (0.12), residues: 1899 sheet: 0.01 (0.19), residues: 740 loop : -0.52 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 203 HIS 0.004 0.001 HIS A 432 PHE 0.022 0.001 PHE A1388 TYR 0.020 0.001 TYR A1177 ARG 0.008 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12504.01 seconds wall clock time: 224 minutes 50.02 seconds (13490.02 seconds total)