Starting phenix.real_space_refine on Mon Mar 25 04:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ir9_9713/03_2024/6ir9_9713.pdb" } resolution = 3.8 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= 0.003 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 266 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28292 2.51 5 N 8212 2.21 5 O 9236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1129": "OD1" <-> "OD2" Residue "A PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1200": "OD1" <-> "OD2" Residue "A PHE 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 6": "NH1" <-> "NH2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 777": "NH1" <-> "NH2" Residue "W PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46231 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11123 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9228 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 52, 'TRANS': 1104} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2610 Classifications: {'DNA': 128} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 127} Chain: "N" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2527 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain breaks: 1 Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2226 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 4 Chain: "a" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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: "V" 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 527 SG CYS A 67 73.622 61.614 137.424 1.00103.22 S ATOM 549 SG CYS A 70 77.089 60.752 138.399 1.00 94.73 S ATOM 594 SG CYS A 77 75.940 64.332 138.881 1.00 74.48 S ATOM 829 SG CYS A 107 78.544 83.381 94.410 1.00142.68 S ATOM 851 SG CYS A 110 79.933 80.030 93.777 1.00152.38 S ATOM 1229 SG CYS A 168 76.676 83.350 91.366 1.00155.44 S ATOM 19883 SG CYS B1163 87.532 61.334 124.895 1.00 76.06 S ATOM 19901 SG CYS B1166 85.696 64.686 123.711 1.00 77.90 S ATOM 20024 SG CYS B1182 83.729 61.187 124.841 1.00108.37 S ATOM 20047 SG CYS B1185 85.974 61.412 121.521 1.00109.59 S ATOM 20992 SG CYS C 85 85.222 77.309 204.161 1.00126.06 S ATOM 21040 SG CYS C 91 80.940 78.189 205.841 1.00108.11 S ATOM 21063 SG CYS C 94 82.478 80.560 202.346 1.00108.09 S ATOM 29171 SG CYS I 78 81.605 167.362 141.310 1.00173.59 S ATOM 29387 SG CYS I 103 81.862 163.727 140.808 1.00166.64 S ATOM 28787 SG CYS I 29 64.050 146.258 100.577 1.00154.71 S ATOM 28812 SG CYS I 32 61.079 148.528 98.884 1.00153.57 S ATOM 29528 SG CYS J 7 86.897 110.737 191.155 1.00 34.60 S ATOM 29551 SG CYS J 10 89.335 110.192 193.835 1.00 33.65 S ATOM 29827 SG CYS J 44 90.298 113.049 191.894 1.00 40.97 S ATOM 29833 SG CYS J 45 87.469 113.026 194.784 1.00 40.49 S ATOM 30995 SG CYS L 33 46.163 95.520 179.886 1.00114.61 S ATOM 31010 SG CYS L 36 44.093 95.899 183.064 1.00124.33 S ATOM 31120 SG CYS L 50 43.546 93.103 180.047 1.00122.63 S ATOM 31144 SG CYS L 53 43.068 97.088 178.900 1.00130.70 S ATOM 36879 SG CYS M 25 52.091 107.333 94.874 1.00198.31 S ATOM 36904 SG CYS M 28 52.062 103.870 94.583 1.00168.76 S ATOM 37062 SG CYS M 49 55.179 105.167 93.723 1.00180.55 S ATOM 37086 SG CYS M 52 52.443 105.565 91.212 1.00191.36 S ATOM 37323 SG CYS V 12 20.851 82.075 115.633 1.00 34.75 S ATOM 37345 SG CYS V 15 21.936 84.905 113.298 1.00 22.76 S ATOM 37447 SG CYS V 29 19.147 85.610 115.248 1.00 18.00 S ATOM 37468 SG CYS V 32 18.769 82.986 112.410 1.00 25.35 S Time building chain proxies: 24.33, per 1000 atoms: 0.53 Number of scatterers: 46231 At special positions: 0 Unit cell: (174.33, 178.8, 229.46, 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 214 16.00 P 266 15.00 Mg 1 11.99 O 9236 8.00 N 8212 7.00 C 28292 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: 20.48 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " Number of angles added : 33 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9588 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 59 sheets defined 43.1% alpha, 17.3% beta 111 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 16.72 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.654A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.560A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 279 removed outlier: 3.510A pdb=" N GLN A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.622A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.585A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.608A pdb=" N GLU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.718A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.502A pdb=" N ALA A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.520A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.947A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.959A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.753A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.582A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.683A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.590A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.737A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.627A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.992A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.633A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.602A pdb=" N GLN A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.594A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.546A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 removed outlier: 3.726A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 removed outlier: 3.897A pdb=" N LYS A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.630A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.566A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.582A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.107A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.664A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1449 through 1454 removed outlier: 3.699A pdb=" N THR A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1456 No H-bonds generated for 'chain 'A' and resid 1455 through 1456' Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.590A pdb=" N TYR A1460 " --> pdb=" O PRO A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.714A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.603A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 312 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.642A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.263A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.907A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.562A pdb=" N ARG B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.690A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.851A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.637A pdb=" N LEU B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.699A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.576A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.909A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.918A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.508A pdb=" N LEU B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.741A pdb=" N LEU C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.695A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.504A pdb=" N GLU C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.523A pdb=" N VAL D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.506A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.772A pdb=" N THR D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.914A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.506A pdb=" N ARG E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 removed outlier: 3.723A pdb=" N ILE E 123 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Proline residue: E 124 - end of helix removed outlier: 4.167A pdb=" N SER E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.507A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.596A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.510A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.623A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 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: 3.931A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.938A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.953A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.616A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.656A pdb=" N ILE M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.725A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.885A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.804A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.618A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 305 through 310' Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.816A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.976A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.737A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.853A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 50 through 77 Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.606A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 74 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.727A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 80 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.667A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.901A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 55 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.826A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.651A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 77 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.566A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.467A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 82 Processing helix chain 'h' and resid 87 through 99 removed outlier: 3.711A pdb=" N ILE h 91 " --> pdb=" O THR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.892A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.763A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.588A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.760A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.560A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.834A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.756A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.467A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.037A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB4, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.837A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.195A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.228A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.582A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.189A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.513A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.037A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.767A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.047A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.555A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.823A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.870A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.926A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.778A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.553A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.643A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.522A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.228A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.638A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AF1, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.865A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.483A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.524A pdb=" N SER I 71 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'M' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF8, first strand: chain 'V' and resid 80 through 86 removed outlier: 7.010A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.542A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.692A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.673A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.670A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'g' and resid 77 through 78 1857 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 558 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 26.97 Time building geometry restraints manager: 22.03 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: 11178 1.33 - 1.45: 10728 1.45 - 1.57: 24825 1.57 - 1.70: 531 1.70 - 1.82: 342 Bond restraints: 47604 Sorted by residual: bond pdb=" C PHE e 84 " pdb=" N GLN e 85 " ideal model delta sigma weight residual 1.331 1.532 -0.201 1.33e-02 5.65e+03 2.29e+02 bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.432 -0.098 1.19e-02 7.06e+03 6.72e+01 bond pdb=" C1' G P 2 " pdb=" N9 G P 2 " ideal model delta sigma weight residual 1.475 1.362 0.113 1.50e-02 4.44e+03 5.66e+01 bond pdb=" C1' G P -1 " pdb=" N9 G P -1 " ideal model delta sigma weight residual 1.475 1.362 0.113 1.50e-02 4.44e+03 5.65e+01 bond pdb=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.480 1.591 -0.111 1.50e-02 4.44e+03 5.48e+01 ... (remaining 47599 not shown) Histogram of bond angle deviations from ideal: 92.28 - 100.70: 254 100.70 - 109.12: 7354 109.12 - 117.54: 28716 117.54 - 125.96: 27747 125.96 - 134.38: 1341 Bond angle restraints: 65412 Sorted by residual: angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" C GLN B 63 " ideal model delta sigma weight residual 108.26 92.28 15.98 1.66e+00 3.63e-01 9.26e+01 angle pdb=" CA PRO W 389 " pdb=" N PRO W 389 " pdb=" CD PRO W 389 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.97e+01 angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta sigma weight residual 110.77 96.75 14.02 1.63e+00 3.76e-01 7.40e+01 angle pdb=" O CYS V 29 " pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 121.31 114.30 7.01 8.50e-01 1.38e+00 6.80e+01 angle pdb=" C ARG W 388 " pdb=" N PRO W 389 " pdb=" CA PRO W 389 " ideal model delta sigma weight residual 119.84 128.76 -8.92 1.25e+00 6.40e-01 5.09e+01 ... (remaining 65407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 26836 34.98 - 69.95: 1511 69.95 - 104.93: 60 104.93 - 139.90: 6 139.90 - 174.88: 2 Dihedral angle restraints: 28415 sinusoidal: 13572 harmonic: 14843 Sorted by residual: dihedral pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta harmonic sigma weight residual 122.80 98.04 24.76 0 2.50e+00 1.60e-01 9.81e+01 dihedral pdb=" CA ARG e 63 " pdb=" C ARG e 63 " pdb=" N LYS e 64 " pdb=" CA LYS e 64 " ideal model delta harmonic sigma weight residual -180.00 -142.22 -37.78 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA ARG a 63 " pdb=" C ARG a 63 " pdb=" N LYS a 64 " pdb=" CA LYS a 64 " ideal model delta harmonic sigma weight residual -180.00 -143.78 -36.22 0 5.00e+00 4.00e-02 5.25e+01 ... (remaining 28412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6921 0.131 - 0.261: 397 0.261 - 0.392: 14 0.392 - 0.523: 2 0.523 - 0.654: 2 Chirality restraints: 7336 Sorted by residual: chirality pdb=" CA GLN B 63 " pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CB GLN B 63 " both_signs ideal model delta sigma weight residual False 2.51 3.16 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 7333 not shown) Planarity restraints: 7519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ILE B 336 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG B 337 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 89 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ASP C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 89 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 88 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 7516 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 671 2.64 - 3.20: 39278 3.20 - 3.77: 72403 3.77 - 4.33: 99235 4.33 - 4.90: 155469 Nonbonded interactions: 367056 Sorted by model distance: nonbonded pdb=" NH1 ARG V 85 " pdb=" OD1 ASP V 87 " model vdw 2.071 2.520 nonbonded pdb=" OE1 GLN M 57 " pdb=" N ASP e 81 " model vdw 2.073 2.520 nonbonded pdb=" O SER M 55 " pdb=" CG LYS f 79 " model vdw 2.074 3.440 nonbonded pdb=" CD1 LEU M 46 " pdb=" OD1 ASP e 81 " model vdw 2.113 3.460 nonbonded pdb=" O2 DC T 18 " pdb=" N2 DG N -18 " model vdw 2.122 2.520 ... (remaining 367051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 31 through 121) selection = chain 'h' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.760 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 147.740 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.260 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 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 : 0.009 0.201 47604 Z= 0.592 Angle : 1.215 19.920 65412 Z= 0.703 Chirality : 0.068 0.654 7336 Planarity : 0.007 0.064 7519 Dihedral : 17.985 174.876 18827 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.30 % Favored : 95.04 % Rotamer: Outliers : 0.74 % Allowed : 3.11 % Favored : 96.15 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.04 % 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: -1.69 (0.10), residues: 5043 helix: -1.29 (0.10), residues: 1856 sheet: -0.75 (0.18), residues: 716 loop : -0.96 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP G 79 HIS 0.014 0.003 HIS f 75 PHE 0.052 0.004 PHE A1176 TYR 0.049 0.004 TYR d 80 ARG 0.016 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 810 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.8462 (t0) cc_final: 0.7824 (t0) REVERT: A 450 SER cc_start: 0.8604 (m) cc_final: 0.8084 (p) REVERT: B 472 VAL cc_start: 0.8999 (t) cc_final: 0.8681 (p) REVERT: B 702 MET cc_start: 0.8421 (tpp) cc_final: 0.7975 (tpp) REVERT: B 1082 MET cc_start: 0.7806 (tpp) cc_final: 0.7559 (tpp) REVERT: B 1136 ASP cc_start: 0.7216 (m-30) cc_final: 0.6703 (m-30) REVERT: C 157 CYS cc_start: 0.7376 (m) cc_final: 0.7119 (m) REVERT: D 170 ASN cc_start: 0.5565 (t0) cc_final: 0.5154 (t0) REVERT: G 29 LYS cc_start: 0.9361 (tptt) cc_final: 0.8923 (tttt) REVERT: G 52 MET cc_start: 0.7425 (mmp) cc_final: 0.6691 (pmm) REVERT: I 68 LEU cc_start: 0.8771 (mt) cc_final: 0.8510 (mm) REVERT: K 6 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.7699 (mmm-85) REVERT: K 31 ILE cc_start: 0.8230 (pt) cc_final: 0.7818 (pt) REVERT: K 33 ILE cc_start: 0.8927 (mp) cc_final: 0.8695 (mp) REVERT: M 31 ASP cc_start: 0.6959 (p0) cc_final: 0.6720 (t0) REVERT: V 107 PRO cc_start: 0.0917 (Cg_exo) cc_final: 0.0476 (Cg_endo) REVERT: W 788 THR cc_start: 0.8449 (m) cc_final: 0.7893 (t) REVERT: W 802 HIS cc_start: 0.7407 (t70) cc_final: 0.6969 (p-80) REVERT: W 804 TRP cc_start: 0.6124 (m100) cc_final: 0.5358 (m100) outliers start: 33 outliers final: 4 residues processed: 838 average time/residue: 0.6751 time to fit residues: 899.7479 Evaluate side-chains 383 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 379 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain b residue 72 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 1.9990 chunk 400 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 413 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 479 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 446 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B 996 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 13 GLN D 38 GLN E 4 ASN E 145 HIS F 100 GLN G 122 ASN H 13 GLN H 44 ASN I 12 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN W 434 ASN c 38 ASN c 73 ASN c 89 ASN d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN f 93 GLN g 112 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 47604 Z= 0.324 Angle : 0.731 14.675 65412 Z= 0.391 Chirality : 0.045 0.186 7336 Planarity : 0.005 0.061 7519 Dihedral : 21.953 177.867 8611 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.74 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 9.40 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: -0.24 (0.11), residues: 5043 helix: 0.42 (0.11), residues: 1902 sheet: -0.44 (0.18), residues: 718 loop : -0.43 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP V 67 HIS 0.019 0.002 HIS A 288 PHE 0.037 0.002 PHE J 59 TYR 0.029 0.002 TYR C 90 ARG 0.017 0.001 ARG V 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 413 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8068 (pt0) REVERT: A 296 LEU cc_start: 0.9044 (tp) cc_final: 0.8789 (tt) REVERT: A 306 ASP cc_start: 0.8362 (t0) cc_final: 0.8075 (t0) REVERT: A 450 SER cc_start: 0.8752 (m) cc_final: 0.8436 (p) REVERT: A 606 MET cc_start: 0.8199 (tpp) cc_final: 0.7968 (tpp) REVERT: A 1410 GLU cc_start: 0.8024 (pm20) cc_final: 0.7609 (pm20) REVERT: A 1411 ILE cc_start: 0.9566 (mm) cc_final: 0.9328 (mt) REVERT: B 702 MET cc_start: 0.8688 (tpp) cc_final: 0.8209 (tpp) REVERT: B 1138 MET cc_start: 0.8182 (mmm) cc_final: 0.7919 (mmm) REVERT: C 66 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8544 (mm) REVERT: D 46 HIS cc_start: 0.5762 (t-170) cc_final: 0.5425 (t-90) REVERT: F 110 ASP cc_start: 0.7549 (p0) cc_final: 0.7284 (p0) REVERT: G 29 LYS cc_start: 0.9429 (tptt) cc_final: 0.9221 (tttt) REVERT: K 6 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: K 31 ILE cc_start: 0.8732 (pt) cc_final: 0.8473 (pt) REVERT: K 33 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8916 (mp) REVERT: M 31 ASP cc_start: 0.7404 (p0) cc_final: 0.7190 (t0) REVERT: M 65 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5979 (mp10) REVERT: W 771 LYS cc_start: 0.9320 (mtpt) cc_final: 0.8657 (ptpt) REVERT: W 802 HIS cc_start: 0.7847 (t70) cc_final: 0.7085 (p-80) REVERT: f 37 LEU cc_start: 0.7288 (tp) cc_final: 0.6782 (tp) REVERT: h 91 ILE cc_start: 0.3223 (mm) cc_final: 0.2803 (mm) outliers start: 84 outliers final: 47 residues processed: 474 average time/residue: 0.5714 time to fit residues: 452.0323 Evaluate side-chains 374 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain h residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 480 optimal weight: 20.0000 chunk 518 optimal weight: 50.0000 chunk 427 optimal weight: 8.9990 chunk 476 optimal weight: 40.0000 chunk 163 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN B 531 ASN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 179 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 44 ASN I 12 ASN I 89 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 GLN W 330 ASN W 339 GLN a 113 HIS c 38 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS g 112 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 47604 Z= 0.320 Angle : 0.680 12.356 65412 Z= 0.360 Chirality : 0.043 0.189 7336 Planarity : 0.005 0.063 7519 Dihedral : 21.783 176.376 8610 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 10.28 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.28 (0.12), residues: 5043 helix: 1.03 (0.12), residues: 1916 sheet: -0.27 (0.18), residues: 728 loop : -0.26 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 209 HIS 0.010 0.001 HIS A 288 PHE 0.026 0.002 PHE J 59 TYR 0.046 0.002 TYR h 80 ARG 0.016 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 335 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.8426 (t0) cc_final: 0.8005 (t0) REVERT: A 450 SER cc_start: 0.8957 (m) cc_final: 0.8627 (p) REVERT: A 606 MET cc_start: 0.8427 (tpp) cc_final: 0.8203 (tpp) REVERT: A 709 MET cc_start: 0.7484 (mmt) cc_final: 0.7106 (mpp) REVERT: A 1128 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 1287 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7002 (mmm) REVERT: B 425 MET cc_start: 0.7269 (mmm) cc_final: 0.7050 (mmm) REVERT: B 702 MET cc_start: 0.8671 (tpp) cc_final: 0.8236 (tpp) REVERT: C 155 ILE cc_start: 0.9124 (pt) cc_final: 0.8873 (mt) REVERT: F 110 ASP cc_start: 0.7719 (p0) cc_final: 0.7385 (p0) REVERT: G 29 LYS cc_start: 0.9459 (tptt) cc_final: 0.9151 (tttt) REVERT: K 6 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7996 (mmm-85) REVERT: M 44 ILE cc_start: 0.8190 (mm) cc_final: 0.7551 (mm) REVERT: W 802 HIS cc_start: 0.7827 (t70) cc_final: 0.7110 (p-80) REVERT: g 57 TYR cc_start: 0.5102 (t80) cc_final: 0.3876 (m-80) outliers start: 103 outliers final: 53 residues processed: 409 average time/residue: 0.5500 time to fit residues: 379.2553 Evaluate side-chains 345 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 290 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain V residue 49 CYS Chi-restraints excluded: chain W residue 259 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain g residue 31 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 50.0000 chunk 361 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 322 optimal weight: 7.9990 chunk 482 optimal weight: 50.0000 chunk 510 optimal weight: 0.0020 chunk 251 optimal weight: 6.9990 chunk 456 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN I 12 ASN I 64 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN d 79 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 47604 Z= 0.219 Angle : 0.604 18.282 65412 Z= 0.319 Chirality : 0.041 0.245 7336 Planarity : 0.004 0.038 7519 Dihedral : 21.650 176.486 8608 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 11.60 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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 (0.12), residues: 5043 helix: 1.34 (0.12), residues: 1922 sheet: -0.18 (0.18), residues: 731 loop : -0.11 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 139 HIS 0.016 0.001 HIS g 31 PHE 0.020 0.001 PHE J 59 TYR 0.018 0.001 TYR a 41 ARG 0.009 0.000 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 317 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.8483 (t0) cc_final: 0.8246 (t0) REVERT: A 450 SER cc_start: 0.8883 (m) cc_final: 0.8535 (p) REVERT: A 960 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8387 (t) REVERT: A 1287 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6938 (mmm) REVERT: A 1410 GLU cc_start: 0.7979 (pm20) cc_final: 0.7711 (pm20) REVERT: B 245 MET cc_start: 0.7991 (tmm) cc_final: 0.7543 (tmm) REVERT: B 702 MET cc_start: 0.8602 (tpp) cc_final: 0.8243 (tpp) REVERT: B 893 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8246 (mm) REVERT: F 110 ASP cc_start: 0.7699 (p0) cc_final: 0.7373 (p0) REVERT: G 29 LYS cc_start: 0.9484 (tptt) cc_final: 0.9207 (tttt) REVERT: W 802 HIS cc_start: 0.7755 (t70) cc_final: 0.7088 (p-80) REVERT: g 57 TYR cc_start: 0.5093 (t80) cc_final: 0.3722 (m-80) outliers start: 91 outliers final: 57 residues processed: 383 average time/residue: 0.5629 time to fit residues: 366.8898 Evaluate side-chains 347 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 287 time to evaluate : 6.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 30.0000 chunk 289 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 435 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 0.0870 chunk 458 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 GLN W 339 GLN d 64 ASN g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 47604 Z= 0.419 Angle : 0.708 12.989 65412 Z= 0.369 Chirality : 0.043 0.176 7336 Planarity : 0.004 0.049 7519 Dihedral : 21.736 177.702 8607 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.03 % Favored : 95.80 % Rotamer: Outliers : 2.73 % Allowed : 11.71 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.38 (0.12), residues: 5043 helix: 1.19 (0.12), residues: 1944 sheet: -0.34 (0.18), residues: 740 loop : -0.24 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 139 HIS 0.009 0.002 HIS K 40 PHE 0.028 0.002 PHE B 314 TYR 0.024 0.002 TYR C 90 ARG 0.009 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 294 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7931 (mmt) cc_final: 0.7402 (mmp) REVERT: A 960 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8644 (t) REVERT: A 1128 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8996 (pp) REVERT: A 1287 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6762 (mmm) REVERT: B 702 MET cc_start: 0.8785 (tpp) cc_final: 0.8435 (tpp) REVERT: B 893 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8788 (mm) REVERT: C 20 MET cc_start: 0.8440 (tmm) cc_final: 0.8100 (tmm) REVERT: E 3 ASP cc_start: 0.7794 (t0) cc_final: 0.7556 (t0) REVERT: F 110 ASP cc_start: 0.7748 (p0) cc_final: 0.7342 (p0) REVERT: G 29 LYS cc_start: 0.9432 (tptt) cc_final: 0.9157 (tttt) REVERT: I 68 LEU cc_start: 0.8790 (mt) cc_final: 0.8472 (mt) REVERT: K 6 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: W 802 HIS cc_start: 0.7783 (t70) cc_final: 0.7156 (p-80) outliers start: 122 outliers final: 85 residues processed: 381 average time/residue: 0.5457 time to fit residues: 355.8195 Evaluate side-chains 360 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 271 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 259 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 86 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 6.9990 chunk 459 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 510 optimal weight: 40.0000 chunk 424 optimal weight: 50.0000 chunk 236 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 ASN g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 47604 Z= 0.287 Angle : 0.621 12.323 65412 Z= 0.326 Chirality : 0.042 0.208 7336 Planarity : 0.004 0.042 7519 Dihedral : 21.663 178.354 8607 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 2.26 % Allowed : 12.65 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.58 (0.12), residues: 5043 helix: 1.46 (0.12), residues: 1929 sheet: -0.35 (0.18), residues: 751 loop : -0.18 (0.13), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 PHE 0.018 0.001 PHE C 178 TYR 0.018 0.001 TYR J 21 ARG 0.006 0.000 ARG J 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 292 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7624 (mmt) cc_final: 0.7010 (mmm) REVERT: A 282 MET cc_start: 0.6692 (ppp) cc_final: 0.6279 (ppp) REVERT: A 548 MET cc_start: 0.6672 (mtp) cc_final: 0.6384 (mtp) REVERT: A 839 GLN cc_start: 0.8486 (tp40) cc_final: 0.8210 (tm-30) REVERT: A 960 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (t) REVERT: A 1410 GLU cc_start: 0.8077 (pm20) cc_final: 0.7872 (pm20) REVERT: B 59 ASP cc_start: 0.5606 (OUTLIER) cc_final: 0.5240 (m-30) REVERT: B 245 MET cc_start: 0.8211 (tmm) cc_final: 0.7966 (tmm) REVERT: B 893 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8696 (mm) REVERT: D 46 HIS cc_start: 0.6685 (t-170) cc_final: 0.6124 (t-90) REVERT: F 110 ASP cc_start: 0.7714 (p0) cc_final: 0.7217 (p0) REVERT: G 29 LYS cc_start: 0.9429 (tptt) cc_final: 0.9152 (tttt) REVERT: J 48 MET cc_start: 0.8874 (mmm) cc_final: 0.8224 (mpp) REVERT: K 6 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: L 66 MET cc_start: 0.8616 (ppp) cc_final: 0.8316 (ppp) REVERT: W 802 HIS cc_start: 0.7778 (t70) cc_final: 0.7160 (p-80) REVERT: g 57 TYR cc_start: 0.5485 (t80) cc_final: 0.3838 (m-80) outliers start: 101 outliers final: 74 residues processed: 369 average time/residue: 0.5358 time to fit residues: 338.6693 Evaluate side-chains 354 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 277 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 86 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 291 optimal weight: 40.0000 chunk 373 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 430 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 508 optimal weight: 30.0000 chunk 318 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN I 12 ASN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47604 Z= 0.217 Angle : 0.592 14.380 65412 Z= 0.309 Chirality : 0.041 0.201 7336 Planarity : 0.003 0.043 7519 Dihedral : 21.525 178.473 8607 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 2.17 % Allowed : 13.28 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.74 (0.12), residues: 5043 helix: 1.58 (0.12), residues: 1949 sheet: -0.29 (0.18), residues: 753 loop : -0.09 (0.14), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 PHE 0.015 0.001 PHE B 314 TYR 0.015 0.001 TYR C 90 ARG 0.004 0.000 ARG f 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 294 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7526 (mmt) cc_final: 0.7038 (mmm) REVERT: A 282 MET cc_start: 0.6708 (ppp) cc_final: 0.6301 (ppp) REVERT: A 434 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 839 GLN cc_start: 0.8491 (tp40) cc_final: 0.8140 (tm-30) REVERT: A 960 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (t) REVERT: B 59 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5198 (m-30) REVERT: B 860 MET cc_start: 0.7722 (tmm) cc_final: 0.7244 (tmm) REVERT: B 893 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8647 (mm) REVERT: D 46 HIS cc_start: 0.6657 (t-170) cc_final: 0.6151 (t-90) REVERT: E 131 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8730 (tt) REVERT: F 110 ASP cc_start: 0.7670 (p0) cc_final: 0.7180 (p0) REVERT: G 29 LYS cc_start: 0.9443 (tptt) cc_final: 0.9171 (ttmt) REVERT: J 48 MET cc_start: 0.8814 (mmm) cc_final: 0.8129 (mpp) REVERT: W 802 HIS cc_start: 0.7787 (t70) cc_final: 0.7146 (p-80) REVERT: g 57 TYR cc_start: 0.5360 (t80) cc_final: 0.3766 (m-80) outliers start: 97 outliers final: 67 residues processed: 365 average time/residue: 0.5574 time to fit residues: 345.4580 Evaluate side-chains 348 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 277 time to evaluate : 4.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain b residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 6.9990 chunk 203 optimal weight: 0.0980 chunk 303 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 400 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 47604 Z= 0.300 Angle : 0.644 21.725 65412 Z= 0.332 Chirality : 0.041 0.180 7336 Planarity : 0.004 0.072 7519 Dihedral : 21.498 179.745 8607 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.17 % Allowed : 13.75 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.68 (0.12), residues: 5043 helix: 1.57 (0.12), residues: 1949 sheet: -0.34 (0.19), residues: 765 loop : -0.13 (0.14), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 PHE 0.017 0.001 PHE C 178 TYR 0.016 0.001 TYR B 833 ARG 0.020 0.001 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 289 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7331 (ptm) cc_final: 0.7123 (ptp) REVERT: A 108 MET cc_start: 0.7824 (mmt) cc_final: 0.7333 (mmp) REVERT: A 282 MET cc_start: 0.6826 (ppp) cc_final: 0.6422 (ppp) REVERT: A 434 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 839 GLN cc_start: 0.8503 (tp40) cc_final: 0.8192 (tm-30) REVERT: A 960 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8582 (t) REVERT: B 59 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5730 (m-30) REVERT: B 893 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8773 (mm) REVERT: D 46 HIS cc_start: 0.6714 (t-170) cc_final: 0.6179 (t-90) REVERT: E 131 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8919 (pt) REVERT: F 110 ASP cc_start: 0.7759 (p0) cc_final: 0.7281 (p0) REVERT: G 29 LYS cc_start: 0.9425 (tptt) cc_final: 0.9189 (ttmt) REVERT: J 48 MET cc_start: 0.8870 (mmm) cc_final: 0.8561 (mmm) REVERT: J 65 LEU cc_start: 0.7171 (mm) cc_final: 0.6698 (tp) REVERT: W 802 HIS cc_start: 0.7644 (t70) cc_final: 0.7096 (p-80) REVERT: f 98 TYR cc_start: 0.3832 (m-10) cc_final: 0.3605 (m-80) REVERT: g 57 TYR cc_start: 0.5407 (t80) cc_final: 0.3763 (m-80) outliers start: 97 outliers final: 78 residues processed: 363 average time/residue: 0.5607 time to fit residues: 346.6502 Evaluate side-chains 353 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 271 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain W residue 259 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 50.0000 chunk 487 optimal weight: 40.0000 chunk 444 optimal weight: 9.9990 chunk 474 optimal weight: 50.0000 chunk 285 optimal weight: 40.0000 chunk 206 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 428 optimal weight: 20.0000 chunk 448 optimal weight: 20.0000 chunk 472 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 47604 Z= 0.376 Angle : 0.698 17.410 65412 Z= 0.360 Chirality : 0.043 0.266 7336 Planarity : 0.004 0.058 7519 Dihedral : 21.570 177.909 8607 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 2.24 % Allowed : 13.95 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.49 (0.12), residues: 5043 helix: 1.44 (0.12), residues: 1951 sheet: -0.42 (0.19), residues: 747 loop : -0.29 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 139 HIS 0.009 0.001 HIS K 40 PHE 0.027 0.002 PHE L 69 TYR 0.017 0.002 TYR E 186 ARG 0.008 0.001 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 277 time to evaluate : 5.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7344 (ptm) cc_final: 0.7078 (ptp) REVERT: A 108 MET cc_start: 0.7924 (mmt) cc_final: 0.7391 (mmp) REVERT: A 282 MET cc_start: 0.6725 (ppp) cc_final: 0.6315 (ppp) REVERT: A 434 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 839 GLN cc_start: 0.8553 (tp40) cc_final: 0.8235 (tm-30) REVERT: A 960 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8630 (t) REVERT: A 1065 MET cc_start: 0.8742 (mmm) cc_final: 0.8046 (mmm) REVERT: A 1211 MET cc_start: 0.7837 (tpp) cc_final: 0.7610 (tpp) REVERT: B 59 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6398 (m-30) REVERT: B 613 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (ttp80) REVERT: B 893 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8928 (mm) REVERT: D 46 HIS cc_start: 0.6839 (t-170) cc_final: 0.6248 (t-90) REVERT: E 131 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8830 (tt) REVERT: F 110 ASP cc_start: 0.7697 (p0) cc_final: 0.7198 (p0) REVERT: G 9 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8180 (mm) REVERT: I 97 MET cc_start: 0.7950 (mmp) cc_final: 0.7496 (tpp) REVERT: J 48 MET cc_start: 0.8925 (mmm) cc_final: 0.8606 (mmm) REVERT: K 6 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7730 (mmm-85) REVERT: W 802 HIS cc_start: 0.7725 (t70) cc_final: 0.7318 (p-80) REVERT: f 98 TYR cc_start: 0.4156 (m-10) cc_final: 0.3942 (m-80) outliers start: 100 outliers final: 85 residues processed: 353 average time/residue: 0.5360 time to fit residues: 326.1811 Evaluate side-chains 359 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 268 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 259 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain h residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 10.0000 chunk 501 optimal weight: 40.0000 chunk 306 optimal weight: 0.2980 chunk 237 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 526 optimal weight: 9.9990 chunk 484 optimal weight: 30.0000 chunk 418 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 47604 Z= 0.176 Angle : 0.614 18.354 65412 Z= 0.318 Chirality : 0.041 0.324 7336 Planarity : 0.003 0.046 7519 Dihedral : 21.418 179.037 8607 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.43 % Allowed : 14.78 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.80 (0.12), residues: 5043 helix: 1.67 (0.12), residues: 1946 sheet: -0.29 (0.18), residues: 772 loop : -0.07 (0.14), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 PHE 0.015 0.001 PHE K 58 TYR 0.014 0.001 TYR H 94 ARG 0.010 0.000 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 297 time to evaluate : 5.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.3716 (tpt) cc_final: 0.3225 (tpt) REVERT: A 74 MET cc_start: 0.7290 (ptm) cc_final: 0.7058 (ptp) REVERT: A 108 MET cc_start: 0.7536 (mmt) cc_final: 0.7129 (mmp) REVERT: A 282 MET cc_start: 0.6799 (ppp) cc_final: 0.6387 (ppp) REVERT: A 434 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 709 MET cc_start: 0.7877 (mmm) cc_final: 0.7376 (mpp) REVERT: A 839 GLN cc_start: 0.8422 (tp40) cc_final: 0.8101 (tm-30) REVERT: B 613 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (ttp80) REVERT: B 860 MET cc_start: 0.8092 (tmm) cc_final: 0.7623 (tmm) REVERT: D 46 HIS cc_start: 0.6628 (t-170) cc_final: 0.6070 (t-90) REVERT: F 110 ASP cc_start: 0.7565 (p0) cc_final: 0.7083 (p0) REVERT: G 9 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8147 (mm) REVERT: I 13 MET cc_start: 0.7253 (tpt) cc_final: 0.7033 (tpp) REVERT: J 48 MET cc_start: 0.8757 (mmm) cc_final: 0.8123 (mpp) REVERT: K 6 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: L 70 ASP cc_start: 0.8245 (m-30) cc_final: 0.7953 (m-30) REVERT: W 802 HIS cc_start: 0.7767 (t70) cc_final: 0.7077 (p-80) REVERT: g 57 TYR cc_start: 0.5424 (t80) cc_final: 0.3757 (m-80) outliers start: 64 outliers final: 53 residues processed: 346 average time/residue: 0.5558 time to fit residues: 332.0637 Evaluate side-chains 340 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 285 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 TRP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 9.9990 chunk 446 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 386 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 419 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS C 257 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.099334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066765 restraints weight = 207295.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066415 restraints weight = 127172.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066400 restraints weight = 88880.938| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 47604 Z= 0.363 Angle : 0.690 17.479 65412 Z= 0.355 Chirality : 0.043 0.276 7336 Planarity : 0.004 0.049 7519 Dihedral : 21.454 176.743 8607 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 1.48 % Allowed : 14.82 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.62 (0.12), residues: 5043 helix: 1.55 (0.12), residues: 1954 sheet: -0.37 (0.19), residues: 736 loop : -0.21 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 139 HIS 0.008 0.001 HIS B 887 PHE 0.021 0.002 PHE C 178 TYR 0.018 0.001 TYR E 186 ARG 0.015 0.001 ARG B 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8457.11 seconds wall clock time: 154 minutes 54.23 seconds (9294.23 seconds total)