Starting phenix.real_space_refine on Fri Aug 7 15:11:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4l_39767/08_2026/8z4l_39767.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 89 5.49 5 S 94 5.16 5 C 14033 2.51 5 N 3946 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1107 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1523 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1598 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "H" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4394 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 18, 'TRANS': 537} Chain breaks: 8 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 105 Chain: "I" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1349 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1917 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 7 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1303 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1023 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna2p': 24, 'rna3p': 24} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 857 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 33} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 359 SG CYS A 71 34.531 52.114 183.826 1.00 87.92 S ATOM 433 SG CYS A 81 33.656 51.667 182.434 1.00 78.21 S ATOM 448 SG CYS A 84 33.153 53.602 185.366 1.00 77.01 S ATOM 1655 SG CYS B 71 25.897 75.698 161.117 1.00 74.95 S ATOM 1729 SG CYS B 81 24.208 77.838 159.183 1.00 62.73 S ATOM 1750 SG CYS B 84 26.696 79.340 162.223 1.00 47.13 S ATOM 1770 SG CYS B 87 28.131 78.376 159.428 1.00 57.73 S ATOM 3182 SG CYS C 71 39.730 95.189 136.748 1.00 52.93 S ATOM 3256 SG CYS C 81 39.924 98.277 134.430 1.00 40.13 S ATOM 3277 SG CYS C 84 42.543 97.839 137.250 1.00 34.48 S ATOM 3297 SG CYS C 87 42.610 95.531 134.523 1.00 39.41 S ATOM 4725 SG CYS D 71 75.939 74.109 87.574 1.00 48.86 S ATOM 4799 SG CYS D 81 78.474 72.613 84.786 1.00 54.41 S ATOM 4820 SG CYS D 84 78.261 71.547 87.704 1.00 63.81 S ATOM 4840 SG CYS D 87 75.086 70.678 85.952 1.00 27.80 S ATOM 6268 SG CYS E 71 66.669 49.901 65.552 1.00 69.72 S ATOM 6342 SG CYS E 81 67.288 47.024 63.026 1.00 58.53 S ATOM 6363 SG CYS E 84 66.304 46.173 65.693 1.00 79.57 S ATOM 6383 SG CYS E 87 63.596 48.497 63.831 1.00 38.76 S ATOM 7792 SG CYS F 71 41.766 40.600 43.219 1.00 79.22 S ATOM 7856 SG CYS F 81 39.256 40.217 41.495 1.00 87.00 S ATOM 7871 SG CYS F 84 38.173 41.174 45.185 1.00 79.01 S ATOM 7891 SG CYS F 87 39.183 43.744 43.021 1.00 78.88 S ATOM 9235 SG CYS G 70 36.845 91.984 36.316 1.00 94.28 S ATOM 9340 SG CYS G 85 38.577 88.971 33.712 1.00 98.77 S ATOM 9359 SG CYS G 88 39.935 92.422 35.811 1.00 95.30 S ATOM 16609 SG CYS J 71 62.852 94.205 111.637 1.00 48.54 S ATOM 16683 SG CYS J 81 65.418 95.835 109.218 1.00 44.99 S ATOM 16704 SG CYS J 84 66.660 93.693 112.099 1.00 44.79 S ATOM 16724 SG CYS J 87 64.685 92.036 109.403 1.00 30.99 S Time building chain proxies: 4.38, per 1000 atoms: 0.19 Number of scatterers: 22713 At special positions: 0 Unit cell: (93.1, 119.7, 217.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 94 16.00 P 89 15.00 O 4542 8.00 N 3946 7.00 C 14033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 972.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " Number of angles added : 36 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5042 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 35 sheets defined 35.9% alpha, 20.9% beta 21 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.808A pdb=" N LYS A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 155 through 172 removed outlier: 4.577A pdb=" N SER A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.566A pdb=" N GLY C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.656A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 removed outlier: 3.553A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.612A pdb=" N GLY E 180 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.571A pdb=" N TYR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.920A pdb=" N LYS G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 124 through 141 removed outlier: 3.702A pdb=" N ASN G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 64 through 69 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 107 removed outlier: 3.709A pdb=" N GLU H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.539A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 274 through 278 removed outlier: 3.649A pdb=" N ARG H 278 " --> pdb=" O LYS H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 323 through 332 removed outlier: 4.147A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 330 " --> pdb=" O HIS H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 355 Processing helix chain 'H' and resid 375 through 384 Processing helix chain 'H' and resid 399 through 412 removed outlier: 3.681A pdb=" N GLU H 404 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 482 removed outlier: 3.546A pdb=" N PHE H 474 " --> pdb=" O ASP H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 539 Processing helix chain 'H' and resid 542 through 554 Processing helix chain 'H' and resid 572 through 593 removed outlier: 3.742A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR H 593 " --> pdb=" O SER H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 604 removed outlier: 3.988A pdb=" N ASN H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE H 601 " --> pdb=" O LYS H 597 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN H 604 " --> pdb=" O ASN H 600 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 488 removed outlier: 3.582A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG I 486 " --> pdb=" O TYR I 482 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 593 removed outlier: 4.140A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR I 593 " --> pdb=" O SER I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 604 removed outlier: 3.929A pdb=" N ASN I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 154 through 157 removed outlier: 3.739A pdb=" N ASP J 157 " --> pdb=" O GLN J 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 154 through 157' Processing helix chain 'J' and resid 158 through 172 Processing helix chain 'K' and resid 378 through 386 removed outlier: 3.600A pdb=" N TYR K 382 " --> pdb=" O GLU K 378 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 386 " --> pdb=" O TYR K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'K' and resid 470 through 487 removed outlier: 3.579A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS K 484 " --> pdb=" O GLU K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 Processing helix chain 'K' and resid 541 through 554 removed outlier: 3.598A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 592 removed outlier: 4.026A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 488 removed outlier: 3.555A pdb=" N PHE L 474 " --> pdb=" O ASP L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 523 Processing helix chain 'L' and resid 527 through 540 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 572 through 590 Processing helix chain 'L' and resid 594 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.610A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 122 removed outlier: 3.848A pdb=" N ASP B 131 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.400A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.380A pdb=" N ARG E 115 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU E 136 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER E 117 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS E 119 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR E 132 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG E 121 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 99 through 101 removed outlier: 3.893A pdb=" N MET F 5 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 193 " --> pdb=" O MET F 5 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 122 removed outlier: 6.579A pdb=" N ARG F 115 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU F 136 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER F 117 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 119 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR F 132 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG F 121 " --> pdb=" O SER F 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC3, first strand: chain 'G' and resid 214 through 216 Processing sheet with id=AC4, first strand: chain 'G' and resid 189 through 190 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 5 removed outlier: 6.741A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE H 25 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS H 24 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE H 59 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU H 26 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP H 56 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 140 through 145 removed outlier: 8.743A pdb=" N VAL H 153 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY H 168 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN H 163 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE H 193 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU H 165 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 225 through 228 removed outlier: 6.633A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE H 227 " --> pdb=" O SER H 313 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.642A pdb=" N GLU H 365 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 434 through 436 Processing sheet with id=AD1, first strand: chain 'H' and resid 434 through 436 removed outlier: 4.732A pdb=" N ARG H 451 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG K 451 " --> pdb=" O GLU H 461 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 445 through 447 Processing sheet with id=AD3, first strand: chain 'I' and resid 467 through 469 Processing sheet with id=AD4, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD5, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD6, first strand: chain 'J' and resid 114 through 122 removed outlier: 6.402A pdb=" N ARG J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU J 136 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER J 117 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 134 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.854A pdb=" N GLY K 162 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN K 163 " --> pdb=" O TYR K 191 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE K 193 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU K 165 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 445 through 447 910 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 2.45 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: 5406 1.33 - 1.46: 5566 1.46 - 1.58: 11957 1.58 - 1.71: 177 1.71 - 1.83: 144 Bond restraints: 23250 Sorted by residual: bond pdb=" C LEU G 105 " pdb=" N SER G 106 " ideal model delta sigma weight residual 1.330 1.484 -0.154 1.46e-02 4.69e+03 1.11e+02 bond pdb=" C GLY H 30 " pdb=" N ILE H 31 " ideal model delta sigma weight residual 1.332 1.452 -0.120 1.23e-02 6.61e+03 9.58e+01 bond pdb=" C ILE H 31 " pdb=" N GLU H 32 " ideal model delta sigma weight residual 1.330 1.457 -0.127 1.36e-02 5.41e+03 8.76e+01 bond pdb=" C ASP H 507 " pdb=" N MET H 508 " ideal model delta sigma weight residual 1.331 1.447 -0.116 1.37e-02 5.33e+03 7.12e+01 bond pdb=" C LYS J 33 " pdb=" N ARG J 34 " ideal model delta sigma weight residual 1.332 1.443 -0.111 1.36e-02 5.41e+03 6.65e+01 ... (remaining 23245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 30361 2.80 - 5.61: 1207 5.61 - 8.41: 179 8.41 - 11.22: 13 11.22 - 14.02: 3 Bond angle restraints: 31763 Sorted by residual: angle pdb=" C LEU G 105 " pdb=" N SER G 106 " pdb=" CA SER G 106 " ideal model delta sigma weight residual 122.77 111.48 11.29 1.33e+00 5.65e-01 7.21e+01 angle pdb=" C ASP B 72 " pdb=" CA ASP B 72 " pdb=" CB ASP B 72 " ideal model delta sigma weight residual 111.82 100.72 11.10 1.38e+00 5.25e-01 6.47e+01 angle pdb=" C ARG B 79 " pdb=" N PRO B 80 " pdb=" CA PRO B 80 " ideal model delta sigma weight residual 119.76 127.39 -7.63 1.03e+00 9.43e-01 5.49e+01 angle pdb=" O GLY G 104 " pdb=" C GLY G 104 " pdb=" N LEU G 105 " ideal model delta sigma weight residual 122.50 129.23 -6.73 9.40e-01 1.13e+00 5.13e+01 angle pdb=" C ILE H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta sigma weight residual 122.93 113.70 9.23 1.45e+00 4.76e-01 4.06e+01 ... (remaining 31758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 13484 33.64 - 67.27: 692 67.27 - 100.91: 57 100.91 - 134.54: 2 134.54 - 168.18: 2 Dihedral angle restraints: 14237 sinusoidal: 6457 harmonic: 7780 Sorted by residual: dihedral pdb=" O4' C N -16 " pdb=" C1' C N -16 " pdb=" N1 C N -16 " pdb=" C2 C N -16 " ideal model delta sinusoidal sigma weight residual -128.00 40.18 -168.18 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 34.68 -162.68 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" CD ARG G 103 " pdb=" NE ARG G 103 " pdb=" CZ ARG G 103 " pdb=" NH1 ARG G 103 " ideal model delta sinusoidal sigma weight residual 0.00 -47.94 47.94 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 14234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3230 0.101 - 0.201: 396 0.201 - 0.302: 35 0.302 - 0.403: 7 0.403 - 0.504: 17 Chirality restraints: 3685 Sorted by residual: chirality pdb=" P C M 34 " pdb=" OP1 C M 34 " pdb=" OP2 C M 34 " pdb=" O5' C M 34 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" P C M 10 " pdb=" OP1 C M 10 " pdb=" OP2 C M 10 " pdb=" O5' C M 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" P G M 30 " pdb=" OP1 G M 30 " pdb=" OP2 G M 30 " pdb=" O5' G M 30 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.91e+00 ... (remaining 3682 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 103 " -0.807 9.50e-02 1.11e+02 3.62e-01 7.95e+01 pdb=" NE ARG G 103 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG G 103 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 103 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 103 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 124 " 0.543 9.50e-02 1.11e+02 2.44e-01 3.62e+01 pdb=" NE ARG J 124 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG J 124 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG J 124 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 124 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 83 " 0.512 9.50e-02 1.11e+02 2.30e-01 3.24e+01 pdb=" NE ARG E 83 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 83 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 83 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 83 " 0.019 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 458 2.65 - 3.21: 19637 3.21 - 3.78: 38124 3.78 - 4.34: 53160 4.34 - 4.90: 84725 Nonbonded interactions: 196104 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.088 2.230 nonbonded pdb=" OD1 ASN H 446 " pdb=" N TYR H 450 " model vdw 2.262 3.120 nonbonded pdb=" O LYS L 578 " pdb=" OG1 THR L 582 " model vdw 2.268 3.040 nonbonded pdb=" O SER G 87 " pdb="ZN ZN G 301 " model vdw 2.275 2.230 nonbonded pdb=" O ALA F 99 " pdb=" OG SER G 150 " model vdw 2.280 3.040 ... (remaining 196099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 28 or (resid 29 through 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and (n \ ame N or name CA or name C or name O or name CB )) or resid 79 through 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 94 or (resid 95 through 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 97 through 110 or (resid 111 and (name N or name CA or name C o \ r name O or name CB )) or resid 112 through 190 or (resid 191 and (name N or nam \ e CA or name C or name O or name CB )) or resid 192 through 196 or resid 301)) selection = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 28 or (resid 29 through 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 74 or (resid 75 and (name N or na \ me CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and \ (name N or name CA or name C or name O or name CB )) or resid 79 through 82 or ( \ resid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 th \ rough 94 or (resid 95 through 96 and (name N or name CA or name C or name O or n \ ame CB )) or resid 97 through 110 or (resid 111 and (name N or name CA or name C \ or name O or name CB )) or resid 112 through 122 or (resid 123 and (name N or n \ ame CA or name C or name O or name CB )) or resid 124 or (resid 125 and (name N \ or name CA or name C or name O or name CB )) or resid 126 through 186 or (resid \ 187 and (name N or name CA or name C or name O or name CB )) or resid 188 throug \ h 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) or \ resid 192 through 196 or resid 301)) selection = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 28 or (resid 29 through 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 74 or (resid 75 and (name N or na \ me CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and \ (name N or name CA or name C or name O or name CB )) or resid 79 through 82 or ( \ resid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 th \ rough 94 or (resid 95 through 96 and (name N or name CA or name C or name O or n \ ame CB )) or resid 97 through 110 or (resid 111 and (name N or name CA or name C \ or name O or name CB )) or resid 112 through 122 or (resid 123 and (name N or n \ ame CA or name C or name O or name CB )) or resid 124 or (resid 125 and (name N \ or name CA or name C or name O or name CB )) or resid 126 through 154 or (resid \ 155 and (name N or name CA or name C or name O or name CB )) or resid 156 throug \ h 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 190 or (resid 191 and (name N or name CA or name C or name O o \ r name CB )) or resid 192 through 196 or resid 301)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 28 or (resid 29 through 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 74 or (resid 75 and (name N or na \ me CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and \ (name N or name CA or name C or name O or name CB )) or resid 79 through 82 or ( \ resid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 th \ rough 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) \ or resid 112 through 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 and (name N or name CA or name C or \ name O or name CB )) or resid 126 through 154 or (resid 155 and (name N or name \ CA or name C or name O or name CB )) or resid 156 through 186 or (resid 187 and \ (name N or name CA or name C or name O or name CB )) or resid 188 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 through 196 or resid 301)) selection = (chain 'F' and (resid 3 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 94 or (resid 95 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 122 or (res \ id 123 and (name N or name CA or name C or name O or name CB )) or resid 124 or \ (resid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 \ through 186 or (resid 187 and (name N or name CA or name C or name O or name CB \ )) or resid 188 through 301)) selection = (chain 'J' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 through 82 or (resid 83 and \ (name N or name CA or name C or name O or name CB )) or resid 84 through 94 or ( \ resid 95 through 96 and (name N or name CA or name C or name O or name CB )) or \ resid 97 through 110 or (resid 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or resid 126 through 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 186 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 196 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 479 or (resid \ 480 and (name N or name CA or name C or name O or name CB )) or resid 481 throug \ h 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) or \ resid 486 through 487 or (resid 488 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 569 or (resid 570 and (name N \ or name CA or name C or name O or name CB )) or resid 571 through 577 or (resid \ 578 and (name N or name CA or name C or name O or name CB )) or resid 579 throug \ h 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) or \ resid 593 through 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB )) or resid 598 through 607 or (resid 608 through 609 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 436 through 466 or (resid 467 and (name N or name CA or name C or n \ ame O or name CB )) or resid 468 through 609)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.090 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.162 23283 Z= 0.462 Angle : 1.305 29.539 31799 Z= 0.783 Chirality : 0.074 0.504 3685 Planarity : 0.014 0.362 3736 Dihedral : 18.489 168.178 9195 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 1.54 % Allowed : 26.44 % Favored : 72.01 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.14), residues: 2619 helix: -1.50 (0.15), residues: 843 sheet: -1.69 (0.21), residues: 488 loop : -1.99 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 79 TYR 0.031 0.003 TYR F 19 PHE 0.060 0.005 PHE G 41 TRP 0.031 0.003 TRP I 535 HIS 0.028 0.005 HIS L 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.46 (23250) covalent geometry : angle 1.24365 / 0.78 (31763) hydrogen bonds : bond 0.15965 / 10.88 ( 930) hydrogen bonds : angle 7.98425 / 5.59 ( 2717) metal coordination : bond 0.03762 / 1.85 ( 33) metal coordination : angle 11.80309 / 7.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 486 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.2673 (pt0) cc_final: 0.2436 (pm20) REVERT: A 191 GLU cc_start: 0.7172 (tt0) cc_final: 0.6867 (mt-10) REVERT: C 93 MET cc_start: 0.8311 (mmm) cc_final: 0.8017 (OUTLIER) REVERT: D 33 LYS cc_start: 0.8191 (mttp) cc_final: 0.7728 (mmmt) REVERT: E 83 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7369 (mpp-170) REVERT: E 190 SER cc_start: 0.8831 (p) cc_final: 0.8587 (m) REVERT: G 103 ARG cc_start: 0.7210 (mmm-85) cc_final: 0.6135 (mmp-170) REVERT: G 111 ILE cc_start: 0.8271 (pp) cc_final: 0.8055 (pt) REVERT: G 141 TYR cc_start: 0.8223 (m-80) cc_final: 0.7891 (m-80) REVERT: H 207 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: H 239 LEU cc_start: 0.7969 (tp) cc_final: 0.7486 (tp) REVERT: H 432 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: H 461 GLU cc_start: 0.7093 (tt0) cc_final: 0.6887 (tt0) REVERT: I 469 ASN cc_start: 0.7270 (m-40) cc_final: 0.7065 (m-40) REVERT: I 480 GLU cc_start: 0.6603 (tp30) cc_final: 0.6307 (tm-30) REVERT: I 482 TYR cc_start: 0.6644 (t80) cc_final: 0.6243 (t80) REVERT: J 33 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7646 (mmtm) REVERT: J 152 ASN cc_start: 0.8137 (t0) cc_final: 0.7417 (m-40) REVERT: L 452 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (pp) REVERT: L 468 ILE cc_start: 0.8283 (mp) cc_final: 0.7865 (mm) outliers start: 34 outliers final: 13 residues processed: 508 average time/residue: 0.7028 time to fit residues: 406.3286 Evaluate side-chains 382 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 367 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain L residue 446 ASN Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 HIS B 154 GLN B 178 ASN C 32 GLN C 154 GLN C 178 ASN D 154 GLN E 112 GLN F 171 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN H 50 ASN H 81 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN H 397 HIS ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN I 558 ASN J 45 ASN J 112 GLN K 443 ASN K 446 ASN K 483 ASN L 446 ASN L 510 HIS L 516 ASN L 556 ASN L 596 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.174767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136250 restraints weight = 24690.603| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.53 r_work: 0.3254 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 23283 Z= 0.271 Angle : 0.791 26.208 31799 Z= 0.393 Chirality : 0.047 0.287 3685 Planarity : 0.005 0.060 3736 Dihedral : 15.043 167.151 4263 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.27 % Allowed : 24.08 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 2619 helix: -0.19 (0.16), residues: 874 sheet: -1.21 (0.22), residues: 459 loop : -1.52 (0.15), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 56 TYR 0.031 0.002 TYR H 245 PHE 0.033 0.002 PHE C 103 TRP 0.014 0.002 TRP H 125 HIS 0.009 0.002 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 (23250) covalent geometry : angle 0.72000 / 0.39 (31763) hydrogen bonds : bond 0.05188 / 3.40 ( 930) hydrogen bonds : angle 5.78619 / 4.03 ( 2717) metal coordination : bond 0.01195 / 0.76 ( 33) metal coordination : angle 9.75936 / 5.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 400 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7052 (tttm) REVERT: A 191 GLU cc_start: 0.6959 (tt0) cc_final: 0.6571 (mm-30) REVERT: B 64 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7941 (tttm) REVERT: B 69 ASN cc_start: 0.7737 (t0) cc_final: 0.7395 (t0) REVERT: B 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7969 (t70) REVERT: C 25 ARG cc_start: 0.8467 (ttt-90) cc_final: 0.8144 (ttp80) REVERT: C 34 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8135 (ttp80) REVERT: C 93 MET cc_start: 0.8494 (mmm) cc_final: 0.8240 (mmm) REVERT: C 111 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: D 33 LYS cc_start: 0.8495 (mttp) cc_final: 0.8017 (mmmt) REVERT: D 123 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: D 131 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: E 72 ASP cc_start: 0.8171 (t70) cc_final: 0.7539 (t70) REVERT: E 75 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: E 83 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7817 (mpp-170) REVERT: E 102 ASP cc_start: 0.8512 (m-30) cc_final: 0.8106 (t0) REVERT: E 112 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: E 190 SER cc_start: 0.8864 (p) cc_final: 0.8618 (m) REVERT: E 197 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7483 (ptt90) REVERT: F 92 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7905 (t) REVERT: F 116 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8080 (mt-10) REVERT: F 152 ASN cc_start: 0.7204 (t0) cc_final: 0.6764 (t0) REVERT: G 103 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.6729 (mmp-170) REVERT: G 116 TYR cc_start: 0.8880 (m-80) cc_final: 0.8507 (m-80) REVERT: G 141 TYR cc_start: 0.8153 (m-80) cc_final: 0.7877 (m-80) REVERT: H 91 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: H 135 GLU cc_start: 0.7757 (tt0) cc_final: 0.7373 (tt0) REVERT: H 159 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8137 (t) REVERT: H 277 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7067 (mtm180) REVERT: H 392 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8005 (ttmm) REVERT: J 33 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8112 (mmtm) REVERT: J 137 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: J 152 ASN cc_start: 0.8483 (t0) cc_final: 0.7627 (m-40) REVERT: J 154 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: K 161 ASN cc_start: 0.7770 (t0) cc_final: 0.7044 (p0) REVERT: K 444 MET cc_start: 0.7242 (mtm) cc_final: 0.6642 (mpt) REVERT: K 459 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8073 (pt) REVERT: K 518 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: L 443 ASN cc_start: 0.6329 (m-40) cc_final: 0.5558 (p0) REVERT: L 551 GLN cc_start: 0.7909 (tt0) cc_final: 0.7635 (tt0) REVERT: L 581 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: L 600 ASN cc_start: 0.7340 (m-40) cc_final: 0.6968 (m110) outliers start: 138 outliers final: 41 residues processed: 502 average time/residue: 0.6571 time to fit residues: 377.2317 Evaluate side-chains 426 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 456 SER Chi-restraints excluded: chain K residue 459 ILE Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 124 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN B 154 GLN C 32 GLN C 36 ASN C 45 ASN C 178 ASN D 112 GLN D 154 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN K 483 ASN L 446 ASN L 510 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133114 restraints weight = 24577.254| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.64 r_work: 0.3267 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23283 Z= 0.145 Angle : 0.649 22.071 31799 Z= 0.324 Chirality : 0.042 0.198 3685 Planarity : 0.004 0.042 3736 Dihedral : 14.860 170.588 4239 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.45 % Allowed : 24.35 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 2619 helix: 0.58 (0.17), residues: 876 sheet: -1.03 (0.23), residues: 456 loop : -1.22 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 25 TYR 0.027 0.001 TYR H 245 PHE 0.024 0.002 PHE K 455 TRP 0.010 0.001 TRP H 564 HIS 0.007 0.002 HIS L 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (23250) covalent geometry : angle 0.58442 / 0.32 (31763) hydrogen bonds : bond 0.04478 / 2.95 ( 930) hydrogen bonds : angle 5.29546 / 3.70 ( 2717) metal coordination : bond 0.01299 / 0.72 ( 33) metal coordination : angle 8.41021 / 5.21 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 400 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6996 (tt0) cc_final: 0.6564 (mt-10) REVERT: B 9 TYR cc_start: 0.8602 (m-80) cc_final: 0.8331 (m-80) REVERT: B 64 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7888 (tttm) REVERT: B 69 ASN cc_start: 0.7821 (t0) cc_final: 0.7396 (t0) REVERT: B 171 ASN cc_start: 0.8396 (m-40) cc_final: 0.8176 (m-40) REVERT: C 34 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.8030 (ttp80) REVERT: C 93 MET cc_start: 0.8491 (mmm) cc_final: 0.8202 (mmm) REVERT: C 111 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: D 33 LYS cc_start: 0.8502 (mttp) cc_final: 0.7943 (mmmt) REVERT: D 123 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: D 131 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: E 32 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: E 72 ASP cc_start: 0.8186 (t70) cc_final: 0.7663 (t70) REVERT: E 75 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: E 83 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7586 (mpp-170) REVERT: E 102 ASP cc_start: 0.8454 (m-30) cc_final: 0.8102 (t0) REVERT: E 111 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: E 123 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: E 154 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: F 34 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7744 (mtm110) REVERT: F 41 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7676 (mtmt) REVERT: F 92 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (t) REVERT: F 98 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7776 (ttp-170) REVERT: F 120 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8729 (mp) REVERT: F 137 GLU cc_start: 0.8116 (pt0) cc_final: 0.7823 (pt0) REVERT: G 26 TYR cc_start: 0.6844 (p90) cc_final: 0.6219 (p90) REVERT: G 61 PHE cc_start: 0.6826 (m-80) cc_final: 0.6468 (m-80) REVERT: G 98 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.7986 (mmt90) REVERT: G 103 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6398 (mmp-170) REVERT: G 141 TYR cc_start: 0.8110 (m-80) cc_final: 0.7891 (m-80) REVERT: H 91 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: H 135 GLU cc_start: 0.7739 (tt0) cc_final: 0.7427 (tt0) REVERT: H 277 ARG cc_start: 0.6996 (mtp180) cc_final: 0.6767 (mtm180) REVERT: H 287 ASN cc_start: 0.7394 (t0) cc_final: 0.7180 (t0) REVERT: H 392 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7817 (ttmp) REVERT: H 418 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6661 (tm-30) REVERT: H 453 MET cc_start: 0.8552 (ptm) cc_final: 0.8352 (ptm) REVERT: H 461 GLU cc_start: 0.7201 (tt0) cc_final: 0.6483 (mt-10) REVERT: H 568 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: I 559 THR cc_start: 0.8843 (p) cc_final: 0.8632 (p) REVERT: J 33 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8101 (mmtm) REVERT: J 34 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7326 (ptm-80) REVERT: J 137 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: J 152 ASN cc_start: 0.8332 (t0) cc_final: 0.7500 (m-40) REVERT: K 161 ASN cc_start: 0.7679 (t0) cc_final: 0.6909 (p0) REVERT: K 518 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: K 554 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7430 (ttm110) REVERT: L 443 ASN cc_start: 0.6104 (m-40) cc_final: 0.5331 (p0) REVERT: L 476 MET cc_start: 0.7704 (mmm) cc_final: 0.7492 (mmp) REVERT: L 513 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6537 (mm) REVERT: L 551 GLN cc_start: 0.7780 (tt0) cc_final: 0.7547 (tt0) REVERT: L 581 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: L 600 ASN cc_start: 0.7211 (m-40) cc_final: 0.6942 (m110) outliers start: 120 outliers final: 48 residues processed: 491 average time/residue: 0.6138 time to fit residues: 345.9538 Evaluate side-chains 439 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 371 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 446 ASN Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 199 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN C 32 GLN C 45 ASN C 178 ASN D 154 GLN D 171 ASN F 152 ASN G 99 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 32 GLN J 45 ASN K 522 ASN K 606 ASN L 446 ASN L 472 ASN L 510 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126967 restraints weight = 24463.219| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.67 r_work: 0.3159 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 23283 Z= 0.269 Angle : 0.718 26.023 31799 Z= 0.353 Chirality : 0.046 0.292 3685 Planarity : 0.005 0.044 3736 Dihedral : 14.844 171.361 4239 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.00 % Allowed : 24.85 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2619 helix: 0.73 (0.17), residues: 894 sheet: -0.79 (0.23), residues: 432 loop : -1.22 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 25 TYR 0.020 0.002 TYR H 245 PHE 0.027 0.002 PHE K 455 TRP 0.012 0.002 TRP H 125 HIS 0.008 0.002 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.27 (23250) covalent geometry : angle 0.65164 / 0.35 (31763) hydrogen bonds : bond 0.04587 / 2.99 ( 930) hydrogen bonds : angle 5.20773 / 3.65 ( 2717) metal coordination : bond 0.01136 / 0.75 ( 33) metal coordination : angle 8.96751 / 5.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 370 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7149 (tt0) cc_final: 0.6740 (mt-10) REVERT: B 9 TYR cc_start: 0.8781 (m-80) cc_final: 0.8426 (m-80) REVERT: B 28 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7668 (mtpt) REVERT: B 64 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7972 (tttm) REVERT: B 69 ASN cc_start: 0.7952 (t0) cc_final: 0.7745 (t0) REVERT: C 25 ARG cc_start: 0.8325 (ttt-90) cc_final: 0.7891 (ttt180) REVERT: C 34 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7858 (ttp80) REVERT: C 93 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8270 (mmm) REVERT: C 111 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: D 34 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7742 (ttm110) REVERT: D 123 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: D 131 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (m-30) REVERT: D 192 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: E 5 MET cc_start: 0.8451 (mtm) cc_final: 0.8181 (mtp) REVERT: E 72 ASP cc_start: 0.8167 (t70) cc_final: 0.7821 (t70) REVERT: E 75 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: E 83 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7689 (mpp-170) REVERT: E 102 ASP cc_start: 0.8507 (m-30) cc_final: 0.8087 (t0) REVERT: E 112 GLN cc_start: 0.8533 (mp10) cc_final: 0.8221 (mt0) REVERT: E 123 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: E 154 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: E 170 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: F 41 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7932 (mtmt) REVERT: F 64 LYS cc_start: 0.8359 (tttp) cc_final: 0.8113 (tttt) REVERT: F 92 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7867 (t) REVERT: F 98 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7785 (ttp-170) REVERT: F 120 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8854 (mp) REVERT: G 9 GLU cc_start: 0.7589 (pt0) cc_final: 0.7129 (tt0) REVERT: G 26 TYR cc_start: 0.6952 (p90) cc_final: 0.6604 (p90) REVERT: G 61 PHE cc_start: 0.6950 (m-80) cc_final: 0.6524 (m-80) REVERT: G 98 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.8232 (mmt90) REVERT: G 103 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.6591 (mmp-170) REVERT: G 116 TYR cc_start: 0.8887 (m-80) cc_final: 0.8566 (m-80) REVERT: H 91 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: H 135 GLU cc_start: 0.8075 (tt0) cc_final: 0.7776 (tt0) REVERT: H 287 ASN cc_start: 0.7426 (t0) cc_final: 0.7096 (t0) REVERT: H 392 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7969 (ttmm) REVERT: H 418 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: H 461 GLU cc_start: 0.7149 (tt0) cc_final: 0.6560 (mt-10) REVERT: H 568 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: I 446 ASN cc_start: 0.6754 (p0) cc_final: 0.6105 (p0) REVERT: J 33 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8206 (mmtm) REVERT: J 123 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: J 137 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: J 152 ASN cc_start: 0.8393 (t0) cc_final: 0.7771 (t0) REVERT: J 154 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: K 161 ASN cc_start: 0.7696 (t0) cc_final: 0.6927 (p0) REVERT: K 484 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8210 (tttp) REVERT: K 518 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: K 554 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7460 (ttm110) REVERT: L 443 ASN cc_start: 0.6009 (m-40) cc_final: 0.5184 (p0) REVERT: L 472 ASN cc_start: 0.7816 (m110) cc_final: 0.7522 (m-40) REVERT: L 551 GLN cc_start: 0.7826 (tt0) cc_final: 0.7587 (tt0) REVERT: L 581 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: L 600 ASN cc_start: 0.7328 (m-40) cc_final: 0.7087 (m110) outliers start: 132 outliers final: 57 residues processed: 470 average time/residue: 0.6596 time to fit residues: 352.4854 Evaluate side-chains 431 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 349 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 186 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN C 32 GLN C 178 ASN D 154 GLN F 152 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 145 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN L 446 ASN L 510 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128321 restraints weight = 24280.328| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.65 r_work: 0.3188 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23283 Z= 0.197 Angle : 0.649 23.808 31799 Z= 0.321 Chirality : 0.043 0.243 3685 Planarity : 0.004 0.042 3736 Dihedral : 14.795 172.642 4239 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.09 % Allowed : 25.08 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2619 helix: 0.96 (0.17), residues: 894 sheet: -0.83 (0.23), residues: 430 loop : -1.10 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 25 TYR 0.016 0.001 TYR H 245 PHE 0.026 0.002 PHE K 455 TRP 0.010 0.001 TRP H 564 HIS 0.006 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (23250) covalent geometry : angle 0.58795 / 0.32 (31763) hydrogen bonds : bond 0.04252 / 2.76 ( 930) hydrogen bonds : angle 5.05761 / 3.56 ( 2717) metal coordination : bond 0.00884 / 0.60 ( 33) metal coordination : angle 8.19331 / 4.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 360 time to evaluate : 0.730 Fit side-chains REVERT: A 191 GLU cc_start: 0.7246 (tt0) cc_final: 0.6858 (mt-10) REVERT: B 9 TYR cc_start: 0.8816 (m-80) cc_final: 0.8443 (m-80) REVERT: B 64 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8018 (tttm) REVERT: B 69 ASN cc_start: 0.7976 (t0) cc_final: 0.7757 (t0) REVERT: C 25 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.7949 (ttt180) REVERT: C 34 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.8087 (ttp80) REVERT: C 93 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: C 111 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: D 34 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7732 (ttm110) REVERT: D 123 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: D 192 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: E 5 MET cc_start: 0.8417 (mtm) cc_final: 0.8183 (mtp) REVERT: E 32 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: E 72 ASP cc_start: 0.8195 (t70) cc_final: 0.7905 (t70) REVERT: E 75 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: E 83 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7664 (mpp-170) REVERT: E 102 ASP cc_start: 0.8462 (m-30) cc_final: 0.8100 (t0) REVERT: E 112 GLN cc_start: 0.8555 (mp10) cc_final: 0.8251 (mt0) REVERT: E 123 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: E 154 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: E 170 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: F 41 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7923 (mtmt) REVERT: F 64 LYS cc_start: 0.8370 (tttp) cc_final: 0.8129 (tttt) REVERT: F 92 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7884 (t) REVERT: F 98 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7746 (ttp-170) REVERT: F 120 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 9 GLU cc_start: 0.7641 (pt0) cc_final: 0.7231 (tt0) REVERT: G 61 PHE cc_start: 0.7000 (m-80) cc_final: 0.6560 (m-80) REVERT: G 98 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8249 (mmt90) REVERT: G 103 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.6501 (mmp-170) REVERT: G 116 TYR cc_start: 0.8879 (m-80) cc_final: 0.8518 (m-80) REVERT: H 91 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: H 127 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: H 135 GLU cc_start: 0.8117 (tt0) cc_final: 0.7839 (tt0) REVERT: H 287 ASN cc_start: 0.7507 (t0) cc_final: 0.7197 (t0) REVERT: H 315 SER cc_start: 0.8250 (m) cc_final: 0.7597 (t) REVERT: H 392 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7907 (ttmp) REVERT: H 418 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: H 432 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: H 453 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8527 (ptm) REVERT: H 461 GLU cc_start: 0.7021 (tt0) cc_final: 0.6804 (mt-10) REVERT: H 568 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: I 476 MET cc_start: 0.6333 (ppp) cc_final: 0.6039 (tpt) REVERT: I 477 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6330 (mp) REVERT: J 33 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8172 (mmtm) REVERT: J 123 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: J 137 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: J 152 ASN cc_start: 0.8362 (t0) cc_final: 0.7749 (t0) REVERT: J 154 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: K 161 ASN cc_start: 0.7684 (t0) cc_final: 0.6925 (p0) REVERT: K 484 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8204 (tttp) REVERT: K 518 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: K 554 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7394 (ttm110) REVERT: K 595 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6707 (mtpp) REVERT: L 443 ASN cc_start: 0.6086 (m-40) cc_final: 0.5245 (p0) REVERT: L 513 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6531 (mm) REVERT: L 551 GLN cc_start: 0.7793 (tt0) cc_final: 0.7578 (tt0) REVERT: L 572 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7202 (p) REVERT: L 581 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: L 600 ASN cc_start: 0.7377 (m-40) cc_final: 0.7104 (m110) outliers start: 134 outliers final: 57 residues processed: 459 average time/residue: 0.6694 time to fit residues: 350.5779 Evaluate side-chains 432 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 344 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 514 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 99 optimal weight: 4.9990 chunk 250 optimal weight: 20.0000 chunk 190 optimal weight: 0.5980 chunk 131 optimal weight: 50.0000 chunk 195 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN B 152 ASN B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN F 152 ASN G 99 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN L 510 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127831 restraints weight = 24287.168| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.66 r_work: 0.3180 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23283 Z= 0.202 Angle : 0.645 23.364 31799 Z= 0.319 Chirality : 0.043 0.240 3685 Planarity : 0.004 0.037 3736 Dihedral : 14.745 173.385 4238 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.91 % Allowed : 25.12 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2619 helix: 1.09 (0.17), residues: 894 sheet: -0.81 (0.23), residues: 430 loop : -1.05 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 465 TYR 0.016 0.001 TYR G 141 PHE 0.030 0.002 PHE I 455 TRP 0.009 0.001 TRP H 473 HIS 0.006 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (23250) covalent geometry : angle 0.58741 / 0.32 (31763) hydrogen bonds : bond 0.04191 / 2.72 ( 930) hydrogen bonds : angle 4.97159 / 3.52 ( 2717) metal coordination : bond 0.00884 / 0.61 ( 33) metal coordination : angle 7.92346 / 4.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 370 time to evaluate : 0.887 Fit side-chains REVERT: A 191 GLU cc_start: 0.7255 (tt0) cc_final: 0.6875 (mt-10) REVERT: B 9 TYR cc_start: 0.8837 (m-80) cc_final: 0.8424 (m-80) REVERT: B 64 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: B 69 ASN cc_start: 0.7956 (t0) cc_final: 0.7740 (t0) REVERT: C 25 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.7981 (ttt180) REVERT: C 34 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8094 (ttp80) REVERT: C 93 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: C 111 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 187 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (pp20) REVERT: D 3 LYS cc_start: 0.8508 (mttm) cc_final: 0.7931 (mttm) REVERT: D 34 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7764 (ttm110) REVERT: D 123 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: E 32 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: E 72 ASP cc_start: 0.8212 (t70) cc_final: 0.7939 (t70) REVERT: E 75 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: E 83 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7675 (mpp-170) REVERT: E 102 ASP cc_start: 0.8426 (m-30) cc_final: 0.8055 (t0) REVERT: E 112 GLN cc_start: 0.8587 (mp10) cc_final: 0.8288 (mt0) REVERT: E 123 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: E 154 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 170 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: F 5 MET cc_start: 0.7851 (ttm) cc_final: 0.7593 (ttp) REVERT: F 41 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7919 (mtmt) REVERT: F 64 LYS cc_start: 0.8388 (tttp) cc_final: 0.8130 (tttt) REVERT: F 92 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7920 (t) REVERT: F 120 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8852 (mp) REVERT: F 171 ASN cc_start: 0.7450 (m110) cc_final: 0.7067 (t0) REVERT: G 9 GLU cc_start: 0.7564 (pt0) cc_final: 0.7189 (tt0) REVERT: G 61 PHE cc_start: 0.7104 (m-80) cc_final: 0.6694 (m-80) REVERT: G 73 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7976 (pt) REVERT: G 98 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.8176 (mmt90) REVERT: G 103 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.6309 (mmm160) REVERT: G 109 GLU cc_start: 0.8275 (pt0) cc_final: 0.8016 (pt0) REVERT: G 116 TYR cc_start: 0.8906 (m-80) cc_final: 0.8581 (m-80) REVERT: H 91 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: H 127 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: H 135 GLU cc_start: 0.8099 (tt0) cc_final: 0.7898 (tt0) REVERT: H 287 ASN cc_start: 0.7513 (t0) cc_final: 0.7212 (t0) REVERT: H 392 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7913 (ttmm) REVERT: H 418 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: H 461 GLU cc_start: 0.6907 (tt0) cc_final: 0.6683 (mt-10) REVERT: H 536 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7947 (mt-10) REVERT: H 568 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: I 446 ASN cc_start: 0.6897 (p0) cc_final: 0.6197 (p0) REVERT: I 476 MET cc_start: 0.6385 (ppp) cc_final: 0.5990 (tpt) REVERT: I 477 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6349 (mp) REVERT: I 577 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: I 594 ASP cc_start: 0.8419 (p0) cc_final: 0.8152 (p0) REVERT: J 33 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8216 (mmtm) REVERT: J 123 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: J 137 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: J 152 ASN cc_start: 0.8395 (t0) cc_final: 0.7823 (t0) REVERT: J 154 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: J 156 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7753 (mmmt) REVERT: K 161 ASN cc_start: 0.7676 (t0) cc_final: 0.6930 (p0) REVERT: K 444 MET cc_start: 0.7351 (mmm) cc_final: 0.6231 (mmm) REVERT: K 484 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8247 (tttp) REVERT: K 518 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: K 554 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7410 (ttm110) REVERT: L 443 ASN cc_start: 0.6116 (m-40) cc_final: 0.5467 (p0) REVERT: L 513 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6506 (mm) REVERT: L 572 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7148 (p) REVERT: L 581 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: L 600 ASN cc_start: 0.7357 (m-40) cc_final: 0.7056 (m110) outliers start: 130 outliers final: 63 residues processed: 468 average time/residue: 0.6349 time to fit residues: 339.7039 Evaluate side-chains 443 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 350 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 514 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 78 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 211 optimal weight: 0.0370 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN F 152 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 175 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN L 510 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128758 restraints weight = 24528.752| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.79 r_work: 0.3186 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23283 Z= 0.170 Angle : 0.619 22.015 31799 Z= 0.308 Chirality : 0.042 0.216 3685 Planarity : 0.004 0.041 3736 Dihedral : 14.731 174.062 4238 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.32 % Allowed : 26.40 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2619 helix: 1.22 (0.17), residues: 894 sheet: -0.76 (0.23), residues: 438 loop : -0.95 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 465 TYR 0.022 0.001 TYR G 141 PHE 0.029 0.002 PHE K 455 TRP 0.009 0.001 TRP H 473 HIS 0.004 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23250) covalent geometry : angle 0.56586 / 0.31 (31763) hydrogen bonds : bond 0.04017 / 2.62 ( 930) hydrogen bonds : angle 4.85885 / 3.44 ( 2717) metal coordination : bond 0.00788 / 0.54 ( 33) metal coordination : angle 7.48789 / 4.46 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 364 time to evaluate : 0.908 Fit side-chains REVERT: A 191 GLU cc_start: 0.7279 (tt0) cc_final: 0.6885 (mt-10) REVERT: B 9 TYR cc_start: 0.8851 (m-80) cc_final: 0.8375 (m-80) REVERT: B 64 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: C 25 ARG cc_start: 0.8351 (ttt-90) cc_final: 0.7970 (ttt180) REVERT: C 34 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.8080 (ttp80) REVERT: C 93 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8151 (mmm) REVERT: C 111 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 151 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8453 (p) REVERT: C 187 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: D 3 LYS cc_start: 0.8546 (mttm) cc_final: 0.7873 (mtpt) REVERT: D 34 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7774 (ttm110) REVERT: D 123 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: E 32 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: E 72 ASP cc_start: 0.8219 (t70) cc_final: 0.7937 (t70) REVERT: E 75 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: E 83 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7681 (mpp-170) REVERT: E 102 ASP cc_start: 0.8446 (m-30) cc_final: 0.8077 (t0) REVERT: E 112 GLN cc_start: 0.8599 (mp10) cc_final: 0.8279 (mt0) REVERT: E 123 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: E 154 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: E 170 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: F 5 MET cc_start: 0.7782 (ttm) cc_final: 0.7514 (ttp) REVERT: F 41 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7878 (mtmt) REVERT: F 92 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7907 (t) REVERT: F 98 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7703 (ttp-170) REVERT: F 120 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8830 (mp) REVERT: F 171 ASN cc_start: 0.7430 (m110) cc_final: 0.7070 (t160) REVERT: G 9 GLU cc_start: 0.7605 (pt0) cc_final: 0.7244 (tt0) REVERT: G 61 PHE cc_start: 0.7042 (m-80) cc_final: 0.6618 (m-80) REVERT: G 73 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7908 (pt) REVERT: G 103 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.6324 (mmm160) REVERT: G 109 GLU cc_start: 0.8313 (pt0) cc_final: 0.8110 (pt0) REVERT: H 26 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7544 (tt) REVERT: H 91 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: H 135 GLU cc_start: 0.8092 (tt0) cc_final: 0.7856 (tt0) REVERT: H 287 ASN cc_start: 0.7537 (t0) cc_final: 0.7254 (t0) REVERT: H 392 LYS cc_start: 0.8263 (ttmt) cc_final: 0.8005 (ttmm) REVERT: H 418 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: H 461 GLU cc_start: 0.6989 (tt0) cc_final: 0.6700 (mt-10) REVERT: H 568 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: I 446 ASN cc_start: 0.6809 (p0) cc_final: 0.6293 (p0) REVERT: I 476 MET cc_start: 0.6440 (ppp) cc_final: 0.5854 (tpt) REVERT: I 477 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6344 (mp) REVERT: I 482 TYR cc_start: 0.6921 (t80) cc_final: 0.6192 (t80) REVERT: I 577 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: I 594 ASP cc_start: 0.8431 (p0) cc_final: 0.8181 (p0) REVERT: J 33 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8197 (mmtm) REVERT: J 123 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: J 137 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: J 152 ASN cc_start: 0.8388 (t0) cc_final: 0.7835 (t0) REVERT: J 154 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: K 161 ASN cc_start: 0.7627 (t0) cc_final: 0.6876 (p0) REVERT: K 444 MET cc_start: 0.7607 (mmm) cc_final: 0.6448 (mmm) REVERT: K 484 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8247 (tttp) REVERT: K 518 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: K 554 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7346 (ttm110) REVERT: K 595 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6566 (mtpp) REVERT: L 443 ASN cc_start: 0.6035 (m-40) cc_final: 0.5407 (p0) REVERT: L 518 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: L 572 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.7008 (p) REVERT: L 581 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: L 600 ASN cc_start: 0.7299 (m-40) cc_final: 0.7007 (m110) outliers start: 117 outliers final: 58 residues processed: 452 average time/residue: 0.6398 time to fit residues: 329.2819 Evaluate side-chains 434 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 344 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 514 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 0.0060 chunk 187 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN F 152 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN K 469 ASN L 510 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130225 restraints weight = 24371.455| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.64 r_work: 0.3224 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23283 Z= 0.140 Angle : 0.591 19.968 31799 Z= 0.298 Chirality : 0.041 0.183 3685 Planarity : 0.004 0.035 3736 Dihedral : 14.696 175.064 4238 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.91 % Allowed : 27.17 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2619 helix: 1.40 (0.17), residues: 894 sheet: -0.73 (0.22), residues: 458 loop : -0.89 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 465 TYR 0.019 0.001 TYR G 141 PHE 0.027 0.002 PHE K 455 TRP 0.009 0.001 TRP H 473 HIS 0.003 0.001 HIS H 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (23250) covalent geometry : angle 0.54518 / 0.30 (31763) hydrogen bonds : bond 0.03900 / 2.55 ( 930) hydrogen bonds : angle 4.72428 / 3.35 ( 2717) metal coordination : bond 0.00669 / 0.46 ( 33) metal coordination : angle 6.81213 / 4.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 361 time to evaluate : 0.774 Fit side-chains REVERT: A 191 GLU cc_start: 0.7360 (tt0) cc_final: 0.6958 (mt-10) REVERT: B 9 TYR cc_start: 0.8831 (m-80) cc_final: 0.8231 (m-80) REVERT: C 25 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.7865 (ttt180) REVERT: C 34 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7947 (ttp80) REVERT: C 93 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: C 111 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: C 187 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: D 3 LYS cc_start: 0.8550 (mttm) cc_final: 0.7900 (mtpt) REVERT: D 33 LYS cc_start: 0.8461 (mttp) cc_final: 0.7937 (mmmt) REVERT: D 34 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7880 (tpt90) REVERT: D 123 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: E 5 MET cc_start: 0.8227 (mtm) cc_final: 0.7993 (mtp) REVERT: E 32 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: E 72 ASP cc_start: 0.8217 (t70) cc_final: 0.7936 (t70) REVERT: E 75 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 83 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7661 (mpp-170) REVERT: E 102 ASP cc_start: 0.8429 (m-30) cc_final: 0.8097 (t0) REVERT: E 112 GLN cc_start: 0.8554 (mp10) cc_final: 0.8261 (mt0) REVERT: E 123 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 154 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: E 170 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: F 5 MET cc_start: 0.7751 (ttm) cc_final: 0.7511 (ttp) REVERT: F 41 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: F 92 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7905 (t) REVERT: F 98 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7694 (ttp-170) REVERT: F 120 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8810 (mp) REVERT: F 171 ASN cc_start: 0.7365 (m110) cc_final: 0.7043 (t160) REVERT: F 189 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7640 (mtpm) REVERT: G 9 GLU cc_start: 0.7602 (pt0) cc_final: 0.7293 (tt0) REVERT: G 61 PHE cc_start: 0.7032 (m-80) cc_final: 0.6629 (m-80) REVERT: G 73 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7886 (pt) REVERT: G 103 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.6248 (mmm160) REVERT: G 116 TYR cc_start: 0.8574 (m-80) cc_final: 0.8373 (m-80) REVERT: G 157 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7693 (ttpt) REVERT: H 26 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7661 (tt) REVERT: H 91 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: H 175 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5555 (mt0) REVERT: H 287 ASN cc_start: 0.7521 (t0) cc_final: 0.7284 (t0) REVERT: H 318 LEU cc_start: 0.8685 (mt) cc_final: 0.8484 (tm) REVERT: H 392 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7987 (ttmm) REVERT: H 418 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: H 461 GLU cc_start: 0.6966 (tt0) cc_final: 0.6716 (mt-10) REVERT: H 568 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: I 439 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7354 (mt) REVERT: I 476 MET cc_start: 0.6482 (ppp) cc_final: 0.5829 (tpt) REVERT: I 477 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6319 (mp) REVERT: I 482 TYR cc_start: 0.6901 (t80) cc_final: 0.6182 (t80) REVERT: I 577 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: I 594 ASP cc_start: 0.8337 (p0) cc_final: 0.8123 (p0) REVERT: J 33 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8191 (mmtt) REVERT: J 123 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: J 137 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: J 152 ASN cc_start: 0.8326 (t0) cc_final: 0.7819 (t0) REVERT: J 154 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: K 161 ASN cc_start: 0.7600 (t0) cc_final: 0.6915 (p0) REVERT: K 440 ASN cc_start: 0.6685 (p0) cc_final: 0.6240 (p0) REVERT: K 444 MET cc_start: 0.7701 (mmm) cc_final: 0.6589 (mmm) REVERT: K 465 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7891 (ptp-170) REVERT: K 484 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8262 (tttp) REVERT: K 518 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: K 554 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7344 (ttm110) REVERT: L 443 ASN cc_start: 0.6063 (m-40) cc_final: 0.5490 (p0) REVERT: L 518 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: L 581 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: L 600 ASN cc_start: 0.7326 (m-40) cc_final: 0.7031 (m110) outliers start: 108 outliers final: 46 residues processed: 441 average time/residue: 0.6447 time to fit residues: 324.1631 Evaluate side-chains 426 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 350 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 175 GLN Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 145 optimal weight: 2.9990 chunk 160 optimal weight: 0.0000 chunk 97 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 60 optimal weight: 0.0010 chunk 248 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN B 171 ASN C 32 GLN D 154 GLN F 152 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 175 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.171676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131001 restraints weight = 24612.412| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.83 r_work: 0.3215 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23283 Z= 0.136 Angle : 0.591 19.412 31799 Z= 0.298 Chirality : 0.041 0.184 3685 Planarity : 0.004 0.040 3736 Dihedral : 14.672 175.398 4236 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.00 % Allowed : 27.99 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2619 helix: 1.48 (0.17), residues: 894 sheet: -0.71 (0.22), residues: 466 loop : -0.86 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 34 TYR 0.026 0.001 TYR G 141 PHE 0.029 0.002 PHE K 455 TRP 0.009 0.001 TRP H 473 HIS 0.003 0.001 HIS H 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (23250) covalent geometry : angle 0.54820 / 0.30 (31763) hydrogen bonds : bond 0.03848 / 2.52 ( 930) hydrogen bonds : angle 4.65615 / 3.31 ( 2717) metal coordination : bond 0.00642 / 0.44 ( 33) metal coordination : angle 6.60866 / 3.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 367 time to evaluate : 0.889 Fit side-chains REVERT: B 9 TYR cc_start: 0.8833 (m-80) cc_final: 0.8181 (m-80) REVERT: C 25 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.7876 (ttt180) REVERT: C 34 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7944 (ttp80) REVERT: C 93 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (mmt) REVERT: C 111 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: C 187 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: D 3 LYS cc_start: 0.8527 (mttm) cc_final: 0.7876 (mtpt) REVERT: D 33 LYS cc_start: 0.8450 (mttp) cc_final: 0.8200 (mtpt) REVERT: D 34 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7884 (tpt90) REVERT: D 123 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: E 5 MET cc_start: 0.8275 (mtm) cc_final: 0.8052 (mtp) REVERT: E 32 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: E 72 ASP cc_start: 0.8161 (t70) cc_final: 0.7885 (t70) REVERT: E 75 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 83 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7675 (mpp-170) REVERT: E 102 ASP cc_start: 0.8450 (m-30) cc_final: 0.8107 (t0) REVERT: E 111 GLU cc_start: 0.8570 (mp0) cc_final: 0.8261 (pm20) REVERT: E 112 GLN cc_start: 0.8568 (mp10) cc_final: 0.8291 (mt0) REVERT: E 154 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: E 170 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: F 5 MET cc_start: 0.7738 (ttm) cc_final: 0.7472 (ttp) REVERT: F 41 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7866 (mtmt) REVERT: F 92 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7922 (t) REVERT: F 98 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7685 (ttp-170) REVERT: F 120 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8820 (mp) REVERT: F 171 ASN cc_start: 0.7371 (m110) cc_final: 0.7043 (t160) REVERT: F 189 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7626 (mtpm) REVERT: G 9 GLU cc_start: 0.7582 (pt0) cc_final: 0.7308 (tt0) REVERT: G 61 PHE cc_start: 0.7074 (m-80) cc_final: 0.6735 (m-80) REVERT: G 73 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7855 (pt) REVERT: G 103 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.6233 (mmm160) REVERT: G 116 TYR cc_start: 0.8598 (m-80) cc_final: 0.8389 (m-80) REVERT: G 157 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7681 (ttpt) REVERT: H 26 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7687 (tt) REVERT: H 91 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: H 287 ASN cc_start: 0.7468 (t0) cc_final: 0.7211 (t0) REVERT: H 392 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7995 (ttmm) REVERT: H 418 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: H 445 CYS cc_start: 0.7831 (p) cc_final: 0.7374 (m) REVERT: H 461 GLU cc_start: 0.6971 (tt0) cc_final: 0.6732 (mt-10) REVERT: H 568 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: I 439 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7386 (mt) REVERT: I 476 MET cc_start: 0.6524 (ppp) cc_final: 0.5829 (tpt) REVERT: I 477 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6250 (mp) REVERT: I 482 TYR cc_start: 0.6889 (t80) cc_final: 0.6182 (t80) REVERT: I 577 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: I 592 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8037 (mtmt) REVERT: I 594 ASP cc_start: 0.8340 (p0) cc_final: 0.8125 (p0) REVERT: J 33 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8190 (mmtt) REVERT: J 123 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: J 137 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: J 152 ASN cc_start: 0.8306 (t0) cc_final: 0.7907 (t0) REVERT: J 154 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: K 161 ASN cc_start: 0.7604 (t0) cc_final: 0.6954 (p0) REVERT: K 440 ASN cc_start: 0.6673 (p0) cc_final: 0.6195 (p0) REVERT: K 444 MET cc_start: 0.7711 (mmm) cc_final: 0.6625 (mmm) REVERT: K 465 ARG cc_start: 0.8297 (ptp90) cc_final: 0.7861 (ptp-170) REVERT: K 484 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8263 (tttp) REVERT: K 518 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: K 554 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7328 (ttm110) REVERT: L 443 ASN cc_start: 0.6025 (m-40) cc_final: 0.5419 (p0) REVERT: L 518 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: L 572 THR cc_start: 0.7175 (OUTLIER) cc_final: 0.6924 (p) REVERT: L 581 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: L 585 ASN cc_start: 0.7355 (m-40) cc_final: 0.7089 (m110) REVERT: L 600 ASN cc_start: 0.7278 (m-40) cc_final: 0.6971 (m110) outliers start: 88 outliers final: 45 residues processed: 434 average time/residue: 0.6352 time to fit residues: 314.6672 Evaluate side-chains 427 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 88 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 175 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128316 restraints weight = 24487.237| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.78 r_work: 0.3184 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23283 Z= 0.202 Angle : 0.638 21.209 31799 Z= 0.316 Chirality : 0.043 0.227 3685 Planarity : 0.004 0.047 3736 Dihedral : 14.650 174.847 4236 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.77 % Allowed : 28.58 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2619 helix: 1.44 (0.17), residues: 894 sheet: -0.73 (0.22), residues: 469 loop : -0.87 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 34 TYR 0.028 0.001 TYR G 141 PHE 0.046 0.002 PHE H 249 TRP 0.009 0.001 TRP H 125 HIS 0.004 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (23250) covalent geometry : angle 0.59159 / 0.31 (31763) hydrogen bonds : bond 0.03930 / 2.56 ( 930) hydrogen bonds : angle 4.72023 / 3.36 ( 2717) metal coordination : bond 0.00813 / 0.56 ( 33) metal coordination : angle 7.10305 / 4.22 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 358 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: B 9 TYR cc_start: 0.8861 (m-80) cc_final: 0.8266 (m-80) REVERT: C 25 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7866 (ttt180) REVERT: C 34 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7951 (ttp80) REVERT: C 93 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8253 (mmm) REVERT: C 111 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: C 187 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7634 (pp20) REVERT: D 3 LYS cc_start: 0.8547 (mttm) cc_final: 0.7885 (mtpt) REVERT: D 34 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (ttm110) REVERT: D 123 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: E 5 MET cc_start: 0.8380 (mtm) cc_final: 0.8110 (mtp) REVERT: E 32 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: E 72 ASP cc_start: 0.8156 (t70) cc_final: 0.7899 (t70) REVERT: E 75 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: E 83 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7669 (mpp-170) REVERT: E 102 ASP cc_start: 0.8463 (m-30) cc_final: 0.8095 (t0) REVERT: E 111 GLU cc_start: 0.8469 (mp0) cc_final: 0.8072 (pm20) REVERT: E 154 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: E 170 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: F 5 MET cc_start: 0.7769 (ttm) cc_final: 0.7520 (ttp) REVERT: F 41 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7868 (mtmt) REVERT: F 92 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7864 (t) REVERT: F 98 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7701 (ttp-170) REVERT: F 120 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8830 (mp) REVERT: F 171 ASN cc_start: 0.7386 (m110) cc_final: 0.7090 (t160) REVERT: F 189 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7646 (mtpm) REVERT: G 9 GLU cc_start: 0.7634 (pt0) cc_final: 0.7340 (tt0) REVERT: G 61 PHE cc_start: 0.7152 (m-80) cc_final: 0.6796 (m-80) REVERT: G 73 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7888 (pt) REVERT: G 103 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.6258 (mmm160) REVERT: G 157 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7720 (ttpt) REVERT: H 26 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7735 (tt) REVERT: H 91 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: H 287 ASN cc_start: 0.7528 (t0) cc_final: 0.7280 (t0) REVERT: H 392 LYS cc_start: 0.8253 (ttmt) cc_final: 0.8016 (ttmm) REVERT: H 418 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: H 445 CYS cc_start: 0.7835 (p) cc_final: 0.7404 (m) REVERT: H 461 GLU cc_start: 0.6977 (tt0) cc_final: 0.6719 (mt-10) REVERT: H 568 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: I 439 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7477 (mt) REVERT: I 476 MET cc_start: 0.6514 (ppp) cc_final: 0.5857 (tpt) REVERT: I 477 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6275 (mp) REVERT: I 577 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: I 592 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8152 (mtmt) REVERT: J 33 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8198 (mmtt) REVERT: J 62 MET cc_start: 0.9060 (mtp) cc_final: 0.8812 (mtp) REVERT: J 123 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: J 137 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: J 152 ASN cc_start: 0.8337 (t0) cc_final: 0.7840 (t0) REVERT: J 154 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: K 161 ASN cc_start: 0.7600 (t0) cc_final: 0.6933 (p0) REVERT: K 440 ASN cc_start: 0.6749 (p0) cc_final: 0.6324 (p0) REVERT: K 444 MET cc_start: 0.7785 (mmm) cc_final: 0.6694 (mmm) REVERT: K 484 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8265 (tttp) REVERT: K 518 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: K 554 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7348 (ttm110) REVERT: K 595 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6307 (tttm) REVERT: L 443 ASN cc_start: 0.5961 (m-40) cc_final: 0.5462 (p0) REVERT: L 518 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: L 572 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6901 (p) REVERT: L 581 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: L 585 ASN cc_start: 0.7392 (m-40) cc_final: 0.7075 (m110) REVERT: L 600 ASN cc_start: 0.7264 (m-40) cc_final: 0.6957 (m110) outliers start: 83 outliers final: 47 residues processed: 418 average time/residue: 0.6264 time to fit residues: 299.1097 Evaluate side-chains 424 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 347 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 237 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN I 558 ASN J 45 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126459 restraints weight = 24467.681| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.83 r_work: 0.3152 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23283 Z= 0.227 Angle : 0.674 23.471 31799 Z= 0.332 Chirality : 0.044 0.269 3685 Planarity : 0.004 0.053 3736 Dihedral : 14.667 174.088 4236 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.04 % Allowed : 28.08 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2619 helix: 1.39 (0.17), residues: 894 sheet: -0.63 (0.22), residues: 448 loop : -0.90 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 465 TYR 0.024 0.001 TYR G 141 PHE 0.034 0.002 PHE H 249 TRP 0.009 0.001 TRP A 176 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (23250) covalent geometry : angle 0.62206 / 0.33 (31763) hydrogen bonds : bond 0.04099 / 2.65 ( 930) hydrogen bonds : angle 4.82465 / 3.44 ( 2717) metal coordination : bond 0.00947 / 0.66 ( 33) metal coordination : angle 7.72139 / 4.61 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7992.86 seconds wall clock time: 137 minutes 5.13 seconds (8225.13 seconds total)