Starting phenix.real_space_refine on Sat Feb 24 19:50:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j4x_0672/02_2024/6j4x_0672.pdb" } resolution = 4.3 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 264 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28267 2.51 5 N 8207 2.21 5 O 9222 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" Residue "e PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46185 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11116 Classifications: {'peptide': 1411} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1342} 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_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2589 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Chain: "N" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2509 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} 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 73.577 60.508 140.102 1.00103.22 S ATOM 549 SG CYS A 70 77.057 59.634 141.022 1.00 94.73 S ATOM 594 SG CYS A 77 75.918 63.210 141.554 1.00 74.48 S ATOM 829 SG CYS A 107 77.945 82.686 97.238 1.00142.68 S ATOM 851 SG CYS A 110 79.324 79.340 96.554 1.00152.38 S ATOM 1222 SG CYS A 168 76.038 82.685 94.220 1.00155.44 S ATOM 19876 SG CYS B1163 87.319 60.338 127.387 1.00 76.06 S ATOM 19894 SG CYS B1166 85.470 63.703 126.260 1.00 77.90 S ATOM 20017 SG CYS B1182 83.516 60.195 127.381 1.00108.37 S ATOM 20040 SG CYS B1185 85.716 60.449 124.035 1.00109.59 S ATOM 20985 SG CYS C 85 86.079 75.547 206.827 1.00126.06 S ATOM 21033 SG CYS C 91 81.822 76.415 208.572 1.00108.11 S ATOM 21056 SG CYS C 94 83.315 78.818 205.080 1.00108.09 S ATOM 29164 SG CYS I 78 81.707 166.207 144.902 1.00173.59 S ATOM 29380 SG CYS I 103 81.954 162.577 144.361 1.00166.64 S ATOM 28780 SG CYS I 29 63.593 145.512 104.205 1.00154.71 S ATOM 28805 SG CYS I 32 60.601 147.800 102.574 1.00153.57 S ATOM 29521 SG CYS J 7 87.611 109.099 194.123 1.00 34.60 S ATOM 29544 SG CYS J 10 90.084 108.526 196.764 1.00 33.65 S ATOM 29820 SG CYS J 44 91.024 111.401 194.839 1.00 40.97 S ATOM 29826 SG CYS J 45 88.234 111.352 197.765 1.00 40.49 S ATOM 30988 SG CYS L 33 46.718 94.023 183.252 1.00114.61 S ATOM 31003 SG CYS L 36 44.691 94.373 186.460 1.00124.33 S ATOM 31113 SG CYS L 50 44.100 91.607 183.424 1.00122.63 S ATOM 31137 SG CYS L 53 43.611 95.602 182.322 1.00130.70 S ATOM 36833 SG CYS M 25 52.353 106.665 98.282 1.00198.31 S ATOM 36858 SG CYS M 28 52.687 103.230 97.876 1.00168.76 S ATOM 37016 SG CYS M 49 55.560 104.895 96.820 1.00180.55 S ATOM 37040 SG CYS M 52 52.600 105.042 94.545 1.00191.36 S ATOM 37277 SG CYS V 12 20.540 81.220 119.214 1.00 34.75 S ATOM 37299 SG CYS V 15 21.596 84.072 116.893 1.00 22.76 S ATOM 37401 SG CYS V 29 18.834 84.760 118.886 1.00 18.00 S ATOM 37422 SG CYS V 32 18.415 82.163 116.029 1.00 25.35 S Time building chain proxies: 23.39, per 1000 atoms: 0.51 Number of scatterers: 46185 At special positions: 0 Unit cell: (174.33, 177.31, 232.44, 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 264 15.00 Mg 1 11.99 O 9222 8.00 N 8207 7.00 C 28267 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: 21.21 Conformation dependent library (CDL) restraints added in 7.1 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 B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " 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 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9586 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 60 sheets defined 43.1% alpha, 17.3% beta 108 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 17.10 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: 3.652A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.041A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.559A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.508A 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: 3.681A 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: 3.501A 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: 3.519A 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: 3.958A 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: 3.754A 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: 3.583A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.589A 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: 4.736A 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: 3.626A 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: 3.991A 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: 3.632A 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: 3.601A 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: 3.565A 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: 3.665A 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: 3.591A 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: 3.715A 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: 3.602A 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: 3.643A 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: 4.262A 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: 3.906A 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: 3.563A 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: 3.773A 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: 3.504A 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: 3.577A 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: 3.907A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.917A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.507A 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: 3.742A 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: 3.696A 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: 3.577A 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: 3.522A 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: 3.508A 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: 3.913A 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: 4.262A 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: 3.507A 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: 3.597A 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: 3.511A 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: 3.622A 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: 3.933A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.954A 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: 3.615A 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: 3.724A 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: 3.884A 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: 3.619A 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: 3.817A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.977A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.736A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.854A 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: 3.608A 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: 3.725A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.665A 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: 3.567A 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: 3.997A 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: 3.589A 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: 3.761A 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: 3.561A 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: 6.126A 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: 6.273A 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: 3.755A 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: 6.466A 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: 4.175A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.412A 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: 4.976A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.741A 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: 7.035A 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: 4.196A 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: 3.581A 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: 4.602A 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: 4.648A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.806A 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: 3.833A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.381A 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: 3.514A 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: 3.510A 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: 6.898A 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: 6.881A 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: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.169A 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: 6.881A 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: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.169A 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: 5.340A 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: 6.671A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.824A 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: 7.013A 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: 4.922A 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: 6.927A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.806A 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: 5.195A 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: 5.237A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.779A 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: 3.535A 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: 4.521A 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: 4.229A 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: 5.866A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.011A 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: 6.589A 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: 3.920A 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: 3.838A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.801A 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: 6.860A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.756A 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: 6.541A 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 'e' and resid 83 through 84 removed outlier: 7.328A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, 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=AG5 Processing sheet with id=AG6, 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: 275 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 32.80 Time building geometry restraints manager: 22.46 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: 10797 1.33 - 1.45: 10971 1.45 - 1.57: 24917 1.57 - 1.70: 527 1.70 - 1.82: 342 Bond restraints: 47554 Sorted by residual: 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 6.75e+01 bond pdb=" C1' G P -2 " pdb=" N9 G P -2 " ideal model delta sigma weight residual 1.475 1.361 0.114 1.50e-02 4.44e+03 5.74e+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 5.70e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.21e-02 6.83e+03 5.52e+01 bond pdb=" C1' U P 4 " pdb=" N1 U P 4 " ideal model delta sigma weight residual 1.480 1.583 -0.103 1.50e-02 4.44e+03 4.70e+01 ... (remaining 47549 not shown) Histogram of bond angle deviations from ideal: 92.33 - 100.74: 256 100.74 - 109.15: 7432 109.15 - 117.56: 28631 117.56 - 125.97: 27679 125.97 - 134.38: 1338 Bond angle restraints: 65336 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 92.33 15.93 1.66e+00 3.63e-01 9.21e+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 99.51 12.49 1.40e+00 5.10e-01 7.96e+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 96.80 13.97 1.63e+00 3.76e-01 7.35e+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 119.84 128.69 -8.85 1.25e+00 6.40e-01 5.02e+01 ... (remaining 65331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 26819 34.97 - 69.94: 1501 69.94 - 104.92: 60 104.92 - 139.89: 6 139.89 - 174.86: 1 Dihedral angle restraints: 28387 sinusoidal: 13547 harmonic: 14840 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 98.11 24.69 0 2.50e+00 1.60e-01 9.75e+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 -142.31 -37.69 0 5.00e+00 4.00e-02 5.68e+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 -143.86 -36.14 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 28384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 6896 0.130 - 0.259: 414 0.259 - 0.389: 12 0.389 - 0.519: 2 0.519 - 0.648: 2 Chirality restraints: 7326 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 1.05e+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 2.05 0.59 2.00e-01 2.50e+01 8.73e+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 4.58e+00 ... (remaining 7323 not shown) Planarity restraints: 7516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.06e-02 3.67e+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 3.69e-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 3.67e-02 1.35e+01 pdb=" C GLU C 88 " 0.063 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 7513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 113 2.42 - 3.04: 26535 3.04 - 3.66: 69184 3.66 - 4.28: 104166 4.28 - 4.90: 166465 Nonbonded interactions: 366463 Sorted by model distance: nonbonded pdb=" O2 DC T 18 " pdb=" N2 DG N -18 " model vdw 1.803 2.520 nonbonded pdb=" NH1 ARG V 85 " pdb=" OD1 ASP V 87 " model vdw 2.071 2.520 nonbonded pdb=" CD ARG B 337 " pdb=" OE1 GLU M 78 " model vdw 2.125 3.440 nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.148 2.170 nonbonded pdb=" O3' G P 10 " pdb="MG MG A1803 " model vdw 2.158 2.170 ... (remaining 366458 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: 0.810 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: 0.040 Extract box with map and model: 5.820 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 154.260 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 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 0.114 47554 Z= 0.584 Angle : 1.215 19.901 65336 Z= 0.702 Chirality : 0.068 0.648 7326 Planarity : 0.007 0.064 7516 Dihedral : 17.936 174.862 18801 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.26 % Favored : 95.08 % Rotamer: Outliers : 0.74 % Allowed : 3.13 % Favored : 96.13 % 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: -1.67 (0.11), residues: 5042 helix: -1.28 (0.10), residues: 1854 sheet: -0.74 (0.18), residues: 715 loop : -0.95 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP G 79 HIS 0.014 0.003 HIS f 75 PHE 0.052 0.004 PHE A1176 TYR 0.050 0.004 TYR d 80 ARG 0.016 0.001 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 654 time to evaluate : 5.635 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.6829 (m-30) cc_final: 0.6605 (m-30) REVERT: A 709 MET cc_start: 0.6841 (mtt) cc_final: 0.6555 (mpp) REVERT: A 844 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7902 (mmmm) REVERT: A 1065 MET cc_start: 0.7846 (mmm) cc_final: 0.7569 (mmm) REVERT: A 1072 GLN cc_start: 0.8251 (mt0) cc_final: 0.7939 (mt0) REVERT: A 1447 MET cc_start: 0.7573 (mmp) cc_final: 0.6336 (mmm) REVERT: B 183 MET cc_start: 0.7202 (mmm) cc_final: 0.6768 (mmp) REVERT: B 302 MET cc_start: 0.8164 (ttm) cc_final: 0.7942 (ttp) REVERT: B 486 SER cc_start: 0.8753 (m) cc_final: 0.8531 (p) REVERT: B 1098 MET cc_start: 0.6819 (mtm) cc_final: 0.6469 (mtp) REVERT: B 1138 MET cc_start: 0.6970 (mmm) cc_final: 0.6736 (mmm) REVERT: C 36 MET cc_start: 0.7436 (mtm) cc_final: 0.7183 (mtm) REVERT: D 46 HIS cc_start: 0.6349 (t-170) cc_final: 0.6109 (t70) REVERT: H 120 LEU cc_start: 0.8231 (mp) cc_final: 0.7972 (tt) REVERT: I 33 ASP cc_start: 0.8229 (m-30) cc_final: 0.7859 (p0) REVERT: I 68 LEU cc_start: 0.8196 (mt) cc_final: 0.7869 (mt) REVERT: W 788 THR cc_start: 0.8426 (m) cc_final: 0.8024 (t) outliers start: 33 outliers final: 7 residues processed: 682 average time/residue: 0.6443 time to fit residues: 695.9375 Evaluate side-chains 331 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 324 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.2980 chunk 400 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 413 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 40.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN B 794 ASN B 887 HIS B 975 GLN B 996 HIS C 13 GLN E 145 HIS E 178 GLN H 13 GLN M 29 ASN M 57 GLN W 330 ASN W 339 GLN W 434 ASN W 784 ASN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 82 HIS c 89 ASN d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 47554 Z= 0.292 Angle : 0.704 9.051 65336 Z= 0.380 Chirality : 0.044 0.299 7326 Planarity : 0.005 0.061 7516 Dihedral : 21.883 175.879 8580 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.76 % Favored : 97.01 % Rotamer: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.87 % 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: -0.11 (0.11), residues: 5042 helix: 0.56 (0.11), residues: 1892 sheet: -0.26 (0.18), residues: 732 loop : -0.40 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 67 HIS 0.010 0.001 HIS B1015 PHE 0.056 0.002 PHE A1169 TYR 0.030 0.002 TYR I 27 ARG 0.014 0.001 ARG B 904 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 383 time to evaluate : 4.889 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.8197 (ptm) cc_final: 0.4690 (ptp) REVERT: A 709 MET cc_start: 0.7381 (mtt) cc_final: 0.7147 (mtm) REVERT: A 1072 GLN cc_start: 0.8162 (mt0) cc_final: 0.7900 (mt0) REVERT: A 1112 ASN cc_start: 0.8858 (p0) cc_final: 0.8414 (p0) REVERT: B 486 SER cc_start: 0.8887 (m) cc_final: 0.8418 (p) REVERT: B 809 MET cc_start: 0.7609 (mtm) cc_final: 0.7386 (mtt) REVERT: B 1098 MET cc_start: 0.6941 (mtm) cc_final: 0.6468 (mtp) REVERT: B 1100 ASP cc_start: 0.8495 (p0) cc_final: 0.8054 (p0) REVERT: C 32 LEU cc_start: 0.8001 (tp) cc_final: 0.7598 (tp) REVERT: C 36 MET cc_start: 0.7667 (mtm) cc_final: 0.7195 (mtm) REVERT: D 46 HIS cc_start: 0.6467 (t-170) cc_final: 0.6130 (t70) REVERT: E 73 ASP cc_start: 0.7744 (p0) cc_final: 0.7465 (p0) REVERT: I 33 ASP cc_start: 0.8084 (m-30) cc_final: 0.7813 (p0) REVERT: I 64 GLN cc_start: 0.7017 (mt0) cc_final: 0.6629 (mp10) REVERT: L 70 ASP cc_start: 0.8488 (t0) cc_final: 0.8037 (t0) REVERT: W 782 LEU cc_start: 0.8364 (mp) cc_final: 0.7903 (mp) REVERT: a 56 LYS cc_start: 0.6340 (mptt) cc_final: 0.5863 (mmtm) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.6226 time to fit residues: 388.6411 Evaluate side-chains 269 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 399 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 480 optimal weight: 20.0000 chunk 518 optimal weight: 50.0000 chunk 427 optimal weight: 1.9990 chunk 476 optimal weight: 40.0000 chunk 163 optimal weight: 40.0000 chunk 385 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 590 GLN A 737 ASN A 967 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS F 100 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN V 43 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN f 27 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 47554 Z= 0.304 Angle : 0.655 9.706 65336 Z= 0.353 Chirality : 0.042 0.195 7326 Planarity : 0.004 0.111 7516 Dihedral : 21.826 175.607 8580 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.07 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % 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: 5042 helix: 1.18 (0.12), residues: 1905 sheet: -0.19 (0.19), residues: 730 loop : -0.27 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 170 HIS 0.009 0.001 HIS A 83 PHE 0.039 0.002 PHE A 445 TYR 0.019 0.002 TYR B1092 ARG 0.014 0.001 ARG a 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 320 time to evaluate : 5.694 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 41 MET cc_start: 0.0241 (tpt) cc_final: -0.3705 (tpt) REVERT: A 488 MET cc_start: 0.8351 (ttt) cc_final: 0.8097 (ttt) REVERT: A 505 LEU cc_start: 0.9022 (tt) cc_final: 0.8659 (mm) REVERT: A 839 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: A 1072 GLN cc_start: 0.8345 (mt0) cc_final: 0.8141 (mt0) REVERT: A 1112 ASN cc_start: 0.8887 (p0) cc_final: 0.8407 (p0) REVERT: A 1371 MET cc_start: 0.8675 (mpp) cc_final: 0.7815 (mtm) REVERT: B 305 MET cc_start: 0.8484 (tpp) cc_final: 0.8209 (tpp) REVERT: B 860 MET cc_start: 0.8609 (tmm) cc_final: 0.8110 (tmm) REVERT: B 968 MET cc_start: 0.7655 (tmm) cc_final: 0.7305 (tmm) REVERT: B 1100 ASP cc_start: 0.8714 (p0) cc_final: 0.8071 (p0) REVERT: B 1101 ASP cc_start: 0.8802 (m-30) cc_final: 0.8556 (m-30) REVERT: B 1138 MET cc_start: 0.7022 (tpp) cc_final: 0.6778 (tpp) REVERT: C 32 LEU cc_start: 0.7967 (tp) cc_final: 0.7760 (tp) REVERT: C 36 MET cc_start: 0.7632 (mtm) cc_final: 0.7279 (mtm) REVERT: D 46 HIS cc_start: 0.6192 (t-170) cc_final: 0.5865 (t70) REVERT: E 73 ASP cc_start: 0.7554 (p0) cc_final: 0.7202 (p0) REVERT: F 93 ILE cc_start: 0.9355 (pt) cc_final: 0.9116 (pt) REVERT: I 64 GLN cc_start: 0.6558 (mt0) cc_final: 0.6323 (mp10) REVERT: J 48 MET cc_start: 0.9146 (mmm) cc_final: 0.8874 (mmm) REVERT: a 56 LYS cc_start: 0.6265 (mptt) cc_final: 0.5777 (mmtm) REVERT: e 120 MET cc_start: 0.8615 (mmm) cc_final: 0.7855 (mmt) REVERT: f 84 MET cc_start: 0.7921 (mmp) cc_final: 0.7716 (mmp) REVERT: h 116 THR cc_start: 0.4874 (m) cc_final: 0.4661 (p) outliers start: 4 outliers final: 0 residues processed: 321 average time/residue: 0.6048 time to fit residues: 321.3558 Evaluate side-chains 251 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 482 optimal weight: 6.9990 chunk 510 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- 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 737 ASN A 787 HIS A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS D 46 HIS D 172 GLN E 135 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** 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: 0.6446 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47554 Z= 0.232 Angle : 0.584 9.253 65336 Z= 0.318 Chirality : 0.041 0.172 7326 Planarity : 0.004 0.080 7516 Dihedral : 21.744 175.666 8580 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.63 (0.12), residues: 5042 helix: 1.44 (0.12), residues: 1927 sheet: -0.21 (0.18), residues: 770 loop : -0.12 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.007 0.001 HIS G 14 PHE 0.023 0.001 PHE K 7 TYR 0.022 0.001 TYR A 37 ARG 0.028 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.0679 (tpt) cc_final: 0.0278 (tpt) REVERT: A 488 MET cc_start: 0.8023 (ttt) cc_final: 0.7690 (mtp) REVERT: A 505 LEU cc_start: 0.8899 (tt) cc_final: 0.8633 (mm) REVERT: A 839 GLN cc_start: 0.8813 (pm20) cc_final: 0.8438 (pm20) REVERT: A 1114 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8618 (tppp) REVERT: A 1433 LEU cc_start: 0.8764 (pp) cc_final: 0.8405 (pp) REVERT: B 860 MET cc_start: 0.8575 (tmm) cc_final: 0.8083 (tmm) REVERT: B 1021 MET cc_start: 0.8159 (mpp) cc_final: 0.7816 (mpp) REVERT: B 1100 ASP cc_start: 0.8753 (p0) cc_final: 0.8087 (p0) REVERT: B 1101 ASP cc_start: 0.8889 (m-30) cc_final: 0.7981 (m-30) REVERT: C 32 LEU cc_start: 0.7796 (tp) cc_final: 0.7534 (tp) REVERT: C 36 MET cc_start: 0.7672 (mtm) cc_final: 0.7329 (mtm) REVERT: C 79 MET cc_start: 0.8053 (tpp) cc_final: 0.7825 (tpp) REVERT: C 138 TYR cc_start: 0.7528 (p90) cc_final: 0.7235 (p90) REVERT: E 73 ASP cc_start: 0.7919 (p0) cc_final: 0.7612 (p0) REVERT: F 93 ILE cc_start: 0.9280 (pt) cc_final: 0.9059 (pt) REVERT: I 64 GLN cc_start: 0.6510 (mt0) cc_final: 0.6231 (mp10) REVERT: J 48 MET cc_start: 0.9201 (mmm) cc_final: 0.8979 (mmm) REVERT: L 70 ASP cc_start: 0.8351 (t0) cc_final: 0.8004 (t0) REVERT: e 120 MET cc_start: 0.8586 (mmm) cc_final: 0.7923 (mmt) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.5823 time to fit residues: 309.3514 Evaluate side-chains 244 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 7 optimal weight: 30.0000 chunk 380 optimal weight: 7.9990 chunk 210 optimal weight: 0.0980 chunk 435 optimal weight: 30.0000 chunk 352 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 458 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 737 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN D 172 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 89 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 ASN ** 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: 0.6520 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47554 Z= 0.273 Angle : 0.619 10.016 65336 Z= 0.331 Chirality : 0.041 0.160 7326 Planarity : 0.004 0.045 7516 Dihedral : 21.735 176.653 8580 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.37 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.66 (0.12), residues: 5042 helix: 1.48 (0.12), residues: 1945 sheet: -0.22 (0.19), residues: 744 loop : -0.13 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 139 HIS 0.009 0.001 HIS D 46 PHE 0.032 0.002 PHE A 445 TYR 0.018 0.002 TYR B1092 ARG 0.014 0.001 ARG B1183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 5.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.0952 (tpt) cc_final: -0.0498 (tpt) REVERT: A 709 MET cc_start: 0.7317 (mmm) cc_final: 0.6786 (ttm) REVERT: A 839 GLN cc_start: 0.8888 (pm20) cc_final: 0.8455 (pm20) REVERT: A 1074 ILE cc_start: 0.8936 (mm) cc_final: 0.8723 (tp) REVERT: A 1371 MET cc_start: 0.8783 (mpp) cc_final: 0.7515 (mtm) REVERT: A 1436 LEU cc_start: 0.9476 (tp) cc_final: 0.9229 (tt) REVERT: B 789 MET cc_start: 0.8108 (mmp) cc_final: 0.7631 (mmm) REVERT: B 1021 MET cc_start: 0.8196 (mpp) cc_final: 0.7749 (mpp) REVERT: B 1098 MET cc_start: 0.6989 (mpp) cc_final: 0.6672 (mpp) REVERT: B 1100 ASP cc_start: 0.8499 (p0) cc_final: 0.7966 (p0) REVERT: B 1101 ASP cc_start: 0.8878 (m-30) cc_final: 0.8617 (m-30) REVERT: C 32 LEU cc_start: 0.7868 (tp) cc_final: 0.7479 (tp) REVERT: C 36 MET cc_start: 0.7656 (mtm) cc_final: 0.7298 (mtm) REVERT: E 73 ASP cc_start: 0.7993 (p0) cc_final: 0.7622 (p0) REVERT: F 93 ILE cc_start: 0.9259 (pt) cc_final: 0.9049 (pt) REVERT: I 64 GLN cc_start: 0.6405 (mt0) cc_final: 0.6019 (mp10) REVERT: J 48 MET cc_start: 0.9229 (mmm) cc_final: 0.8977 (mmm) REVERT: e 120 MET cc_start: 0.8633 (mmm) cc_final: 0.8069 (mmt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.5786 time to fit residues: 287.6715 Evaluate side-chains 235 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.4980 chunk 459 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 510 optimal weight: 10.0000 chunk 424 optimal weight: 50.0000 chunk 236 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1190 GLN ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 47554 Z= 0.237 Angle : 0.583 10.925 65336 Z= 0.314 Chirality : 0.041 0.203 7326 Planarity : 0.004 0.070 7516 Dihedral : 21.706 176.925 8580 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 0.74 (0.12), residues: 5042 helix: 1.60 (0.12), residues: 1934 sheet: -0.30 (0.18), residues: 759 loop : -0.08 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 18 HIS 0.010 0.001 HIS A 300 PHE 0.030 0.002 PHE B 278 TYR 0.019 0.001 TYR B1092 ARG 0.018 0.000 ARG V 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 5.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.1380 (tpt) cc_final: 0.0008 (tpt) REVERT: A 709 MET cc_start: 0.7368 (mmm) cc_final: 0.6885 (ttm) REVERT: A 839 GLN cc_start: 0.8842 (pm20) cc_final: 0.8457 (pm20) REVERT: A 1371 MET cc_start: 0.8687 (mpp) cc_final: 0.7543 (mtm) REVERT: B 245 MET cc_start: 0.8269 (tmm) cc_final: 0.7912 (tmm) REVERT: B 1021 MET cc_start: 0.8275 (mpp) cc_final: 0.7773 (mpp) REVERT: B 1098 MET cc_start: 0.6856 (mpp) cc_final: 0.6463 (mpp) REVERT: B 1100 ASP cc_start: 0.8555 (p0) cc_final: 0.7989 (p0) REVERT: B 1101 ASP cc_start: 0.8883 (m-30) cc_final: 0.8508 (m-30) REVERT: C 32 LEU cc_start: 0.7842 (tp) cc_final: 0.7405 (tp) REVERT: C 36 MET cc_start: 0.7651 (mtm) cc_final: 0.7303 (mtm) REVERT: E 73 ASP cc_start: 0.7999 (p0) cc_final: 0.7570 (p0) REVERT: G 52 MET cc_start: 0.8562 (mmp) cc_final: 0.8075 (pmm) REVERT: I 64 GLN cc_start: 0.6522 (mt0) cc_final: 0.6146 (mp10) REVERT: J 48 MET cc_start: 0.9269 (mmm) cc_final: 0.9007 (mmm) REVERT: e 120 MET cc_start: 0.8633 (mmm) cc_final: 0.8087 (mmt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.5849 time to fit residues: 283.7589 Evaluate side-chains 226 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 5.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 291 optimal weight: 40.0000 chunk 373 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 430 optimal weight: 20.0000 chunk 285 optimal weight: 6.9990 chunk 508 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN A 737 ASN A1190 GLN A1208 GLN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 HIS ** 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: 0.6541 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47554 Z= 0.235 Angle : 0.584 10.482 65336 Z= 0.313 Chirality : 0.040 0.154 7326 Planarity : 0.004 0.060 7516 Dihedral : 21.684 177.652 8580 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.75 % 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: 0.81 (0.12), residues: 5042 helix: 1.72 (0.12), residues: 1922 sheet: -0.46 (0.18), residues: 761 loop : -0.01 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 554 HIS 0.006 0.001 HIS b 75 PHE 0.017 0.001 PHE K 105 TYR 0.018 0.001 TYR A1368 ARG 0.010 0.000 ARG e 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 5.210 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: A 41 MET cc_start: 0.1424 (tpt) cc_final: 0.0089 (tpt) REVERT: A 305 MET cc_start: 0.8272 (mmm) cc_final: 0.7696 (mmm) REVERT: A 819 MET cc_start: 0.8384 (mmm) cc_final: 0.7890 (mmt) REVERT: B 860 MET cc_start: 0.8573 (tmm) cc_final: 0.8093 (tmm) REVERT: B 1021 MET cc_start: 0.8381 (mpp) cc_final: 0.7920 (mpp) REVERT: B 1098 MET cc_start: 0.6860 (mpp) cc_final: 0.6422 (mpp) REVERT: B 1100 ASP cc_start: 0.8474 (p0) cc_final: 0.7954 (p0) REVERT: B 1101 ASP cc_start: 0.8779 (m-30) cc_final: 0.8470 (m-30) REVERT: C 32 LEU cc_start: 0.7774 (tp) cc_final: 0.7353 (tp) REVERT: C 36 MET cc_start: 0.7662 (mtm) cc_final: 0.7371 (mtm) REVERT: F 93 ILE cc_start: 0.9304 (pt) cc_final: 0.9061 (pt) REVERT: G 52 MET cc_start: 0.8573 (mmp) cc_final: 0.8055 (pmm) REVERT: I 94 ASP cc_start: 0.7403 (t0) cc_final: 0.6589 (p0) REVERT: J 48 MET cc_start: 0.9261 (mmm) cc_final: 0.8921 (mmm) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.5704 time to fit residues: 275.8405 Evaluate side-chains 223 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 6.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 303 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1190 GLN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN ** d 81 ASN ** 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: 0.6556 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 47554 Z= 0.238 Angle : 0.587 9.986 65336 Z= 0.314 Chirality : 0.041 0.227 7326 Planarity : 0.004 0.043 7516 Dihedral : 21.684 178.019 8580 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 0.02 % Allowed : 0.69 % Favored : 99.28 % 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: 0.78 (0.12), residues: 5042 helix: 1.69 (0.12), residues: 1932 sheet: -0.49 (0.18), residues: 758 loop : -0.03 (0.14), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 554 HIS 0.006 0.001 HIS A 660 PHE 0.022 0.002 PHE K 7 TYR 0.015 0.001 TYR A 37 ARG 0.009 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 5.708 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: A 41 MET cc_start: 0.1330 (tpt) cc_final: 0.0155 (tpt) REVERT: A 819 MET cc_start: 0.8192 (mmm) cc_final: 0.7666 (mmt) REVERT: B 792 MET cc_start: 0.7728 (mpp) cc_final: 0.7507 (mpp) REVERT: B 860 MET cc_start: 0.8535 (tmm) cc_final: 0.8073 (tmm) REVERT: B 1021 MET cc_start: 0.8450 (mpp) cc_final: 0.7936 (mpp) REVERT: B 1098 MET cc_start: 0.7017 (mpp) cc_final: 0.6556 (mpp) REVERT: B 1100 ASP cc_start: 0.8531 (p0) cc_final: 0.8086 (p0) REVERT: B 1101 ASP cc_start: 0.8787 (m-30) cc_final: 0.8418 (m-30) REVERT: C 32 LEU cc_start: 0.7788 (tp) cc_final: 0.7372 (tp) REVERT: C 36 MET cc_start: 0.7662 (mtm) cc_final: 0.7371 (mtm) REVERT: F 93 ILE cc_start: 0.9270 (pt) cc_final: 0.9052 (pt) REVERT: G 23 ASN cc_start: 0.8607 (m-40) cc_final: 0.8292 (t0) REVERT: G 52 MET cc_start: 0.8575 (mmp) cc_final: 0.8018 (pmm) REVERT: J 48 MET cc_start: 0.9220 (mmm) cc_final: 0.8937 (mmm) REVERT: M 46 LEU cc_start: 0.9310 (mm) cc_final: 0.8993 (mm) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.5978 time to fit residues: 285.4748 Evaluate side-chains 224 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 chunk 474 optimal weight: 0.7980 chunk 285 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 428 optimal weight: 40.0000 chunk 448 optimal weight: 40.0000 chunk 472 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1190 GLN B 157 HIS ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** 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: 0.6536 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47554 Z= 0.198 Angle : 0.566 11.198 65336 Z= 0.303 Chirality : 0.040 0.176 7326 Planarity : 0.004 0.047 7516 Dihedral : 21.636 177.944 8580 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.66 % 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: 0.87 (0.12), residues: 5042 helix: 1.81 (0.12), residues: 1928 sheet: -0.49 (0.18), residues: 761 loop : -0.00 (0.14), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 554 HIS 0.006 0.001 HIS J 52 PHE 0.031 0.001 PHE B 278 TYR 0.018 0.001 TYR B 797 ARG 0.013 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 5.032 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 41 MET cc_start: 0.1259 (tpt) cc_final: -0.0034 (tpt) REVERT: A 305 MET cc_start: 0.8353 (mmm) cc_final: 0.8120 (mmm) REVERT: A 709 MET cc_start: 0.6611 (ttp) cc_final: 0.6058 (tmm) REVERT: A 819 MET cc_start: 0.8218 (mmm) cc_final: 0.7688 (mmt) REVERT: A 1436 LEU cc_start: 0.9511 (tp) cc_final: 0.9228 (tt) REVERT: B 860 MET cc_start: 0.8552 (tmm) cc_final: 0.8081 (tmm) REVERT: B 1021 MET cc_start: 0.8381 (mpp) cc_final: 0.8132 (mpp) REVERT: B 1098 MET cc_start: 0.6938 (mpp) cc_final: 0.6338 (mpp) REVERT: B 1100 ASP cc_start: 0.8576 (p0) cc_final: 0.8081 (p0) REVERT: B 1101 ASP cc_start: 0.8836 (m-30) cc_final: 0.8428 (m-30) REVERT: C 32 LEU cc_start: 0.7852 (tp) cc_final: 0.7490 (tp) REVERT: C 36 MET cc_start: 0.7695 (mtm) cc_final: 0.7435 (mtm) REVERT: F 93 ILE cc_start: 0.9222 (pt) cc_final: 0.9013 (pt) REVERT: G 23 ASN cc_start: 0.8584 (m-40) cc_final: 0.8298 (t0) REVERT: G 52 MET cc_start: 0.8507 (mmp) cc_final: 0.7980 (pmm) REVERT: J 48 MET cc_start: 0.9198 (mmm) cc_final: 0.8907 (mmm) REVERT: M 46 LEU cc_start: 0.9292 (mm) cc_final: 0.9004 (mm) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.5549 time to fit residues: 261.9753 Evaluate side-chains 229 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 9.9990 chunk 501 optimal weight: 40.0000 chunk 306 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 484 optimal weight: 10.0000 chunk 418 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 256 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 968 ASN A1190 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN I 22 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** 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: 0.6678 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 47554 Z= 0.395 Angle : 0.736 13.055 65336 Z= 0.388 Chirality : 0.043 0.173 7326 Planarity : 0.005 0.056 7516 Dihedral : 21.912 179.819 8580 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 0.02 % Allowed : 0.25 % Favored : 99.73 % 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: 0.34 (0.12), residues: 5042 helix: 1.28 (0.12), residues: 1962 sheet: -0.69 (0.18), residues: 783 loop : -0.26 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 209 HIS 0.009 0.002 HIS B 97 PHE 0.026 0.002 PHE K 7 TYR 0.022 0.002 TYR A 37 ARG 0.010 0.001 ARG A 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 5.215 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: A 41 MET cc_start: 0.1744 (tpt) cc_final: 0.0483 (tpt) REVERT: A 709 MET cc_start: 0.6671 (ttp) cc_final: 0.5973 (tmm) REVERT: A 819 MET cc_start: 0.8354 (mmm) cc_final: 0.7870 (mmt) REVERT: A 1436 LEU cc_start: 0.9317 (tp) cc_final: 0.9070 (tt) REVERT: B 860 MET cc_start: 0.8622 (tmm) cc_final: 0.8195 (tmm) REVERT: B 1021 MET cc_start: 0.8515 (mpp) cc_final: 0.8053 (mpp) REVERT: B 1100 ASP cc_start: 0.8663 (p0) cc_final: 0.8143 (p0) REVERT: B 1101 ASP cc_start: 0.8847 (m-30) cc_final: 0.8538 (m-30) REVERT: C 20 MET cc_start: 0.8596 (tmm) cc_final: 0.8341 (tmm) REVERT: F 93 ILE cc_start: 0.9308 (pt) cc_final: 0.9084 (pt) REVERT: M 46 LEU cc_start: 0.9034 (mm) cc_final: 0.8643 (mm) REVERT: M 74 ILE cc_start: 0.4770 (mm) cc_final: 0.4512 (mm) REVERT: M 78 GLU cc_start: 0.5506 (mt-10) cc_final: 0.4529 (pp20) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.5626 time to fit residues: 255.9873 Evaluate side-chains 210 residues out of total 4466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 40.0000 chunk 128 optimal weight: 2.9990 chunk 386 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 419 optimal weight: 40.0000 chunk 175 optimal weight: 8.9990 chunk 430 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1190 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN I 22 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.061731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042593 restraints weight = 437795.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043981 restraints weight = 242753.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044024 restraints weight = 162192.500| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47554 Z= 0.254 Angle : 0.617 12.067 65336 Z= 0.329 Chirality : 0.041 0.152 7326 Planarity : 0.004 0.042 7516 Dihedral : 21.898 179.128 8580 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 0.02 % Allowed : 0.16 % Favored : 99.82 % 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: 0.51 (0.12), residues: 5042 helix: 1.48 (0.12), residues: 1970 sheet: -0.72 (0.19), residues: 745 loop : -0.19 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 554 HIS 0.008 0.001 HIS B 97 PHE 0.018 0.002 PHE B 194 TYR 0.015 0.002 TYR B1092 ARG 0.020 0.001 ARG V 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7932.87 seconds wall clock time: 147 minutes 8.35 seconds (8828.35 seconds total)