Starting phenix.real_space_refine on Fri Jan 24 21:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_39767_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_39767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_39767.map" model { file = "/net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_39767_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4l_39767/01_2025/8z4l_39767_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3} 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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 3} 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: {'GLU:plan': 1, 'ASP: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, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'HIS:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} 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: 13.28, per 1000 atoms: 0.58 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: 5.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 9.36 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: 9.46 Time building geometry restraints manager: 6.33 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: 30381 2.80 - 5.61: 1187 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: 3270 0.101 - 0.201: 356 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 196 or resid 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: 5.440 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: 0.000 Extract box with map and model: 1.700 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 61.370 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 0.154 23250 Z= 0.496 Angle : 1.234 14.022 31763 Z= 0.731 Chirality : 0.073 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (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 TRP 0.031 0.003 TRP I 535 HIS 0.028 0.005 HIS L 510 PHE 0.060 0.005 PHE G 41 TYR 0.031 0.003 TYR F 19 ARG 0.020 0.002 ARG C 79 *********************** 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 : 2.469 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: 0.7368 (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: 0.7647 (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: 12 residues processed: 508 average time/residue: 1.5056 time to fit residues: 864.0061 Evaluate side-chains 381 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 367 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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 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 226 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 127 optimal weight: 40.0000 chunk 156 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 119 HIS B 154 GLN B 178 ASN C 32 GLN C 45 ASN C 154 GLN C 178 ASN F 171 ASN G 147 ASN H 50 ASN H 81 ASN H 304 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN J 112 GLN J 171 ASN K 443 ASN K 446 ASN K 483 ASN L 510 HIS L 516 ASN L 556 ASN L 596 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.179441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140973 restraints weight = 24722.854| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.58 r_work: 0.3366 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23250 Z= 0.212 Angle : 0.626 8.015 31763 Z= 0.336 Chirality : 0.042 0.233 3685 Planarity : 0.005 0.060 3736 Dihedral : 15.017 165.080 4261 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.32 % Allowed : 24.85 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 2619 helix: 0.06 (0.17), residues: 876 sheet: -1.15 (0.23), residues: 458 loop : -1.48 (0.15), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 473 HIS 0.008 0.001 HIS L 510 PHE 0.019 0.002 PHE C 103 TYR 0.036 0.001 TYR H 245 ARG 0.006 0.001 ARG F 98 *********************** 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 524 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 407 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6534 (mmtt) REVERT: A 191 GLU cc_start: 0.6914 (tt0) cc_final: 0.6525 (mt-10) REVERT: B 64 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8072 (tttm) REVERT: B 69 ASN cc_start: 0.7596 (t0) cc_final: 0.7160 (t0) REVERT: B 171 ASN cc_start: 0.8438 (m-40) cc_final: 0.8223 (m-40) REVERT: B 179 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8605 (ttmt) REVERT: C 25 ARG cc_start: 0.8333 (ttt-90) cc_final: 0.8044 (ttp80) REVERT: C 34 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.8008 (ttp80) REVERT: C 93 MET cc_start: 0.8300 (mmm) cc_final: 0.7966 (mmm) REVERT: D 33 LYS cc_start: 0.8382 (mttp) cc_final: 0.7867 (mmmt) REVERT: D 123 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 131 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: E 32 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: E 72 ASP cc_start: 0.8121 (t70) cc_final: 0.7514 (t70) REVERT: E 75 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: E 102 ASP cc_start: 0.8448 (m-30) cc_final: 0.8135 (t0) REVERT: E 112 GLN cc_start: 0.8326 (mp10) cc_final: 0.8104 (mt0) REVERT: F 92 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7869 (t) REVERT: F 116 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7985 (mt-10) REVERT: F 152 ASN cc_start: 0.7119 (t0) cc_final: 0.6691 (t0) REVERT: F 187 GLU cc_start: 0.8309 (tp30) cc_final: 0.8107 (mm-30) REVERT: G 26 TYR cc_start: 0.6887 (p90) cc_final: 0.6174 (p90) REVERT: G 103 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.6655 (mmp-170) REVERT: G 141 TYR cc_start: 0.8151 (m-80) cc_final: 0.7896 (m-80) REVERT: H 461 GLU cc_start: 0.7162 (tt0) cc_final: 0.6737 (mt-10) REVERT: H 568 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: I 482 TYR cc_start: 0.6844 (t80) cc_final: 0.6196 (t80) REVERT: J 137 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: J 152 ASN cc_start: 0.8348 (t0) cc_final: 0.7555 (m-40) REVERT: K 161 ASN cc_start: 0.7691 (t0) cc_final: 0.7020 (p0) REVERT: K 459 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8105 (pt) REVERT: K 505 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8087 (mt) REVERT: L 443 ASN cc_start: 0.6276 (m-40) cc_final: 0.5434 (p0) REVERT: L 551 GLN cc_start: 0.7879 (tt0) cc_final: 0.7648 (tt0) REVERT: L 581 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: L 600 ASN cc_start: 0.7283 (m-40) cc_final: 0.6893 (m110) outliers start: 117 outliers final: 31 residues processed: 492 average time/residue: 1.3918 time to fit residues: 781.5018 Evaluate side-chains 405 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 B residue 179 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 192 ASP 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 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 76 SER Chi-restraints excluded: chain E residue 86 THR 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 140 SER Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 568 GLU 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 137 GLU Chi-restraints excluded: chain K residue 456 SER Chi-restraints excluded: chain K residue 459 ILE Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN C 32 GLN C 154 GLN C 178 ASN D 154 GLN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135665 restraints weight = 24432.509| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.57 r_work: 0.3310 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23250 Z= 0.205 Angle : 0.573 6.705 31763 Z= 0.305 Chirality : 0.041 0.232 3685 Planarity : 0.004 0.045 3736 Dihedral : 14.786 167.750 4237 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.09 % Allowed : 25.31 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2619 helix: 0.80 (0.17), residues: 875 sheet: -0.99 (0.23), residues: 448 loop : -1.22 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 473 HIS 0.006 0.001 HIS L 510 PHE 0.016 0.002 PHE G 74 TYR 0.025 0.001 TYR H 245 ARG 0.007 0.000 ARG E 25 *********************** 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 523 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 411 time to evaluate : 2.772 Fit side-chains revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6564 (mmtt) REVERT: A 191 GLU cc_start: 0.7189 (tt0) cc_final: 0.6756 (mt-10) REVERT: A 198 PHE cc_start: 0.7815 (m-80) cc_final: 0.7539 (m-80) REVERT: B 64 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7790 (tttm) REVERT: B 69 ASN cc_start: 0.7535 (t0) cc_final: 0.7131 (t0) REVERT: C 25 ARG cc_start: 0.8278 (ttt-90) cc_final: 0.7907 (ttp80) REVERT: C 34 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.8017 (ttp80) REVERT: C 93 MET cc_start: 0.8437 (mmm) cc_final: 0.8198 (mmm) REVERT: C 111 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 192 ASP cc_start: 0.7969 (m-30) cc_final: 0.7711 (m-30) REVERT: D 33 LYS cc_start: 0.8456 (mttp) cc_final: 0.7924 (mmmt) REVERT: D 123 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: D 131 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: E 5 MET cc_start: 0.8360 (mtm) cc_final: 0.8134 (mtp) REVERT: E 32 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: E 72 ASP cc_start: 0.8097 (t70) cc_final: 0.7673 (t70) REVERT: E 75 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: E 102 ASP cc_start: 0.8436 (m-30) cc_final: 0.8120 (t0) REVERT: E 112 GLN cc_start: 0.8363 (mp10) cc_final: 0.8062 (mt0) REVERT: F 92 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7740 (t) REVERT: F 98 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7873 (ttp-170) REVERT: F 137 GLU cc_start: 0.8100 (pt0) cc_final: 0.7823 (pt0) REVERT: F 152 ASN cc_start: 0.7486 (t0) cc_final: 0.7227 (t0) REVERT: F 187 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: G 26 TYR cc_start: 0.6852 (p90) cc_final: 0.6376 (p90) REVERT: G 61 PHE cc_start: 0.6829 (m-80) cc_final: 0.6498 (m-80) REVERT: G 98 ARG cc_start: 0.8312 (mmt-90) cc_final: 0.8041 (mmt90) REVERT: G 103 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.6419 (mmp-170) REVERT: G 141 TYR cc_start: 0.8083 (m-80) cc_final: 0.7839 (m-80) REVERT: H 135 GLU cc_start: 0.7598 (tt0) cc_final: 0.6815 (mp0) REVERT: H 137 PHE cc_start: 0.6097 (m-80) cc_final: 0.5846 (m-80) REVERT: H 159 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7951 (t) REVERT: H 315 SER cc_start: 0.7963 (p) cc_final: 0.7388 (t) REVERT: H 392 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7762 (ttmm) REVERT: H 432 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: H 453 MET cc_start: 0.8468 (ptm) cc_final: 0.8069 (ptm) REVERT: H 568 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: J 123 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8233 (mt-10) REVERT: J 137 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: J 152 ASN cc_start: 0.8243 (t0) cc_final: 0.7430 (m-40) REVERT: J 154 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: J 156 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7631 (mmmt) REVERT: K 161 ASN cc_start: 0.7614 (t0) cc_final: 0.6912 (p0) REVERT: K 444 MET cc_start: 0.7334 (mtm) cc_final: 0.6889 (mpt) REVERT: K 505 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8066 (mt) REVERT: K 578 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8002 (mppt) REVERT: L 443 ASN cc_start: 0.6064 (m-40) cc_final: 0.5134 (p0) REVERT: L 551 GLN cc_start: 0.7797 (tt0) cc_final: 0.7542 (tt0) REVERT: L 581 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: L 596 ASN cc_start: 0.7862 (t0) cc_final: 0.7577 (t0) REVERT: L 600 ASN cc_start: 0.7302 (m-40) cc_final: 0.7026 (m110) outliers start: 112 outliers final: 36 residues processed: 488 average time/residue: 1.3940 time to fit residues: 776.2112 Evaluate side-chains 417 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 ASN 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 83 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 111 GLU 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 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 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 F residue 187 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 86 THR 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 225 VAL Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 432 GLU 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 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 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 446 ASN Chi-restraints excluded: chain L residue 452 LEU 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 54 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 206 optimal weight: 0.0570 chunk 220 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN C 32 GLN C 36 ASN C 171 ASN C 178 ASN D 154 GLN E 112 GLN 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 I 558 ASN J 32 GLN J 45 ASN K 483 ASN K 522 ASN K 606 ASN L 446 ASN L 510 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131051 restraints weight = 24577.809| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.62 r_work: 0.3234 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23250 Z= 0.279 Angle : 0.584 6.286 31763 Z= 0.309 Chirality : 0.042 0.213 3685 Planarity : 0.004 0.039 3736 Dihedral : 14.759 169.751 4237 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.95 % Allowed : 24.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2619 helix: 1.11 (0.18), residues: 874 sheet: -0.78 (0.23), residues: 439 loop : -1.04 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 125 HIS 0.006 0.001 HIS D 119 PHE 0.023 0.002 PHE K 455 TYR 0.019 0.001 TYR H 245 ARG 0.007 0.001 ARG F 25 *********************** 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 528 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 397 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6978 (tttm) REVERT: A 191 GLU cc_start: 0.7302 (tt0) cc_final: 0.6861 (mm-30) REVERT: A 198 PHE cc_start: 0.7849 (m-80) cc_final: 0.7614 (m-80) REVERT: B 9 TYR cc_start: 0.8692 (m-80) cc_final: 0.8259 (m-80) REVERT: B 69 ASN cc_start: 0.7608 (t0) cc_final: 0.7394 (t0) REVERT: B 72 ASP cc_start: 0.8557 (t70) cc_final: 0.8341 (t0) REVERT: C 25 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.7839 (ttt180) REVERT: C 34 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7959 (ttp80) REVERT: C 93 MET cc_start: 0.8518 (mmm) cc_final: 0.8142 (mmm) REVERT: C 111 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: D 33 LYS cc_start: 0.8510 (mttp) cc_final: 0.7955 (mmmt) REVERT: D 123 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: D 131 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: E 5 MET cc_start: 0.8429 (mtm) cc_final: 0.8204 (mtp) REVERT: E 32 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: E 72 ASP cc_start: 0.8185 (t70) cc_final: 0.7898 (t70) REVERT: E 75 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 102 ASP cc_start: 0.8448 (m-30) cc_final: 0.8118 (t0) REVERT: E 112 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: E 123 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: E 154 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: E 170 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: F 41 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7617 (mtmt) REVERT: F 92 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7835 (t) REVERT: F 98 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7812 (ttp-170) REVERT: F 120 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (mp) REVERT: G 26 TYR cc_start: 0.6982 (p90) cc_final: 0.6733 (p90) REVERT: G 61 PHE cc_start: 0.6981 (m-80) cc_final: 0.6537 (m-80) REVERT: G 98 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8133 (mmt90) REVERT: G 103 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.6517 (mmp-170) REVERT: G 116 TYR cc_start: 0.8824 (m-80) cc_final: 0.8512 (m-80) REVERT: H 54 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7769 (mmtm) REVERT: H 127 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: H 135 GLU cc_start: 0.7838 (tt0) cc_final: 0.7507 (tt0) REVERT: H 159 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7936 (t) REVERT: H 315 SER cc_start: 0.8069 (p) cc_final: 0.7470 (t) REVERT: H 392 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7897 (ttmm) REVERT: H 418 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: H 432 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: H 461 GLU cc_start: 0.7223 (tt0) cc_final: 0.6490 (mt-10) REVERT: H 568 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: I 577 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: J 123 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: J 137 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: J 152 ASN cc_start: 0.8223 (t0) cc_final: 0.7525 (m-40) REVERT: J 156 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7645 (mmmt) REVERT: K 161 ASN cc_start: 0.7640 (t0) cc_final: 0.6936 (p0) REVERT: L 443 ASN cc_start: 0.5985 (m-40) cc_final: 0.5278 (p0) REVERT: L 551 GLN cc_start: 0.7802 (tt0) cc_final: 0.7577 (tt0) REVERT: L 600 ASN cc_start: 0.7302 (m-40) cc_final: 0.6984 (m110) outliers start: 131 outliers final: 42 residues processed: 494 average time/residue: 1.4096 time to fit residues: 794.5424 Evaluate side-chains 417 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain B residue 70 VAL 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 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 111 GLU 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 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 112 GLN 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 120 LEU Chi-restraints excluded: chain G residue 139 LEU 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 54 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 159 THR 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 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 432 GLU Chi-restraints excluded: chain H residue 436 VAL 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 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 57 SER 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 L residue 518 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 165 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN D 171 ASN E 112 GLN F 152 ASN G 99 ASN ** 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** H 551 GLN I 483 ASN J 45 ASN L 510 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129756 restraints weight = 24435.582| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.67 r_work: 0.3207 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23250 Z= 0.285 Angle : 0.580 7.391 31763 Z= 0.306 Chirality : 0.042 0.213 3685 Planarity : 0.004 0.037 3736 Dihedral : 14.758 170.758 4237 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.41 % Allowed : 25.40 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2619 helix: 1.30 (0.18), residues: 873 sheet: -0.79 (0.23), residues: 442 loop : -0.91 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 125 HIS 0.006 0.001 HIS D 119 PHE 0.028 0.002 PHE K 455 TYR 0.016 0.001 TYR G 137 ARG 0.009 0.001 ARG F 25 *********************** 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 498 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 379 time to evaluate : 2.945 Fit side-chains REVERT: A 191 GLU cc_start: 0.7383 (tt0) cc_final: 0.6972 (mt-10) REVERT: A 198 PHE cc_start: 0.7923 (m-80) cc_final: 0.7656 (m-80) REVERT: B 9 TYR cc_start: 0.8822 (m-80) cc_final: 0.8299 (m-80) REVERT: B 69 ASN cc_start: 0.7677 (t0) cc_final: 0.7415 (t0) REVERT: B 72 ASP cc_start: 0.8645 (t70) cc_final: 0.8419 (t0) REVERT: C 25 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.7870 (ttt180) REVERT: C 34 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7976 (ttp80) REVERT: C 93 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: C 111 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: D 3 LYS cc_start: 0.8454 (mttm) cc_final: 0.7877 (mttm) REVERT: D 34 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7756 (ttm110) REVERT: D 123 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: E 5 MET cc_start: 0.8454 (mtm) cc_final: 0.8230 (mtp) REVERT: E 32 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: E 72 ASP cc_start: 0.8181 (t70) cc_final: 0.7954 (t70) REVERT: E 75 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: E 102 ASP cc_start: 0.8452 (m-30) cc_final: 0.8121 (t0) REVERT: E 112 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: E 123 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: E 154 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: E 170 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: F 5 MET cc_start: 0.7837 (ttm) cc_final: 0.7482 (ttp) REVERT: F 41 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (mtmt) REVERT: F 92 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7856 (t) REVERT: F 98 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7808 (ttp-170) REVERT: F 120 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8806 (mp) REVERT: F 171 ASN cc_start: 0.7647 (m110) cc_final: 0.7100 (t160) REVERT: F 187 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8007 (mt-10) REVERT: G 9 GLU cc_start: 0.7375 (pt0) cc_final: 0.7053 (tt0) REVERT: G 61 PHE cc_start: 0.6905 (m-80) cc_final: 0.6442 (m-80) REVERT: G 103 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.6551 (mmp-170) REVERT: H 54 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7716 (mmtm) REVERT: H 127 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: H 135 GLU cc_start: 0.7946 (tt0) cc_final: 0.7590 (tt0) REVERT: H 340 PHE cc_start: 0.8097 (m-80) cc_final: 0.7888 (m-80) REVERT: H 392 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7919 (ttmp) REVERT: H 418 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: H 432 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: H 461 GLU cc_start: 0.7154 (tt0) cc_final: 0.6853 (mt-10) REVERT: H 568 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: I 476 MET cc_start: 0.6288 (ppp) cc_final: 0.5945 (tpt) REVERT: I 477 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6246 (mp) REVERT: I 577 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: J 123 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: J 137 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: J 152 ASN cc_start: 0.8275 (t0) cc_final: 0.7681 (t0) REVERT: J 154 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: J 156 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7732 (mmmt) REVERT: K 444 MET cc_start: 0.7181 (mtm) cc_final: 0.6978 (mmm) REVERT: L 443 ASN cc_start: 0.6026 (m-40) cc_final: 0.5165 (p0) REVERT: L 470 ASP cc_start: 0.8060 (p0) cc_final: 0.7801 (p0) REVERT: L 581 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: L 590 LEU cc_start: 0.8395 (tp) cc_final: 0.8177 (mt) REVERT: L 600 ASN cc_start: 0.7346 (m-40) cc_final: 0.7087 (m110) outliers start: 119 outliers final: 52 residues processed: 464 average time/residue: 1.5025 time to fit residues: 788.5566 Evaluate side-chains 425 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 349 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 70 VAL 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 D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 111 GLU 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 112 GLN 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 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 161 ILE Chi-restraints excluded: chain G residue 124 ASP 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 54 LYS Chi-restraints excluded: chain H residue 86 THR 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 225 VAL Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 432 GLU 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 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 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 K residue 438 ASN Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 514 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 121 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 171 ASN C 32 GLN C 178 ASN D 154 GLN E 112 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 L 510 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127521 restraints weight = 24454.867| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.82 r_work: 0.3151 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 23250 Z= 0.339 Angle : 0.602 8.126 31763 Z= 0.316 Chirality : 0.043 0.213 3685 Planarity : 0.004 0.047 3736 Dihedral : 14.761 170.684 4236 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.59 % Allowed : 25.85 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2619 helix: 1.33 (0.18), residues: 873 sheet: -0.82 (0.23), residues: 444 loop : -0.86 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.006 0.001 HIS D 119 PHE 0.022 0.002 PHE K 455 TYR 0.017 0.001 TYR G 141 ARG 0.011 0.001 ARG F 25 *********************** 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 487 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 364 time to evaluate : 2.825 Fit side-chains REVERT: A 191 GLU cc_start: 0.7419 (tt0) cc_final: 0.7009 (mt-10) REVERT: B 9 TYR cc_start: 0.8893 (m-80) cc_final: 0.8363 (m-80) REVERT: B 69 ASN cc_start: 0.7719 (t0) cc_final: 0.7444 (t0) REVERT: B 72 ASP cc_start: 0.8620 (t70) cc_final: 0.8359 (t0) REVERT: C 25 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.7940 (ttt180) REVERT: C 34 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8086 (ttp80) REVERT: C 93 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8256 (mmm) REVERT: C 187 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: D 3 LYS cc_start: 0.8513 (mttm) cc_final: 0.7844 (mtpt) REVERT: D 34 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7758 (ttm110) REVERT: D 123 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: E 5 MET cc_start: 0.8521 (mtm) cc_final: 0.8312 (mtp) REVERT: E 32 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: E 72 ASP cc_start: 0.8249 (t70) cc_final: 0.8029 (t70) REVERT: E 75 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: E 102 ASP cc_start: 0.8473 (m-30) cc_final: 0.8021 (t0) REVERT: E 112 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: E 123 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: E 154 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: E 170 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: F 5 MET cc_start: 0.7842 (ttm) cc_final: 0.7515 (ttp) REVERT: F 41 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7928 (mtmt) REVERT: F 92 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7905 (t) REVERT: F 98 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.7889 (ttp-170) REVERT: F 120 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8847 (mp) REVERT: F 171 ASN cc_start: 0.7783 (m110) cc_final: 0.7432 (t0) REVERT: F 189 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7775 (mtpm) REVERT: G 9 GLU cc_start: 0.7495 (pt0) cc_final: 0.7248 (tt0) REVERT: G 61 PHE cc_start: 0.7090 (m-80) cc_final: 0.6686 (m-80) REVERT: G 103 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.6401 (mmm160) REVERT: G 112 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: G 124 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.5789 (t0) REVERT: H 54 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7823 (mmtm) REVERT: H 127 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: H 135 GLU cc_start: 0.8125 (tt0) cc_final: 0.7880 (tt0) REVERT: H 315 SER cc_start: 0.8103 (m) cc_final: 0.7713 (m) REVERT: H 392 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7997 (ttmp) REVERT: H 418 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: H 432 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: H 445 CYS cc_start: 0.7811 (p) cc_final: 0.7389 (m) REVERT: H 461 GLU cc_start: 0.7108 (tt0) cc_final: 0.6888 (mt-10) REVERT: H 568 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: I 476 MET cc_start: 0.6311 (ppp) cc_final: 0.5922 (tpt) REVERT: I 477 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6369 (mp) REVERT: I 577 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: J 123 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: J 137 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: J 152 ASN cc_start: 0.8273 (t0) cc_final: 0.7714 (t0) REVERT: J 154 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: K 440 ASN cc_start: 0.7141 (p0) cc_final: 0.6751 (p0) REVERT: K 444 MET cc_start: 0.7140 (mtm) cc_final: 0.6931 (mmm) REVERT: L 443 ASN cc_start: 0.6102 (m-40) cc_final: 0.5243 (p0) REVERT: L 518 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: L 581 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: L 600 ASN cc_start: 0.7400 (m-40) cc_final: 0.7122 (m110) outliers start: 123 outliers final: 63 residues processed: 458 average time/residue: 1.4746 time to fit residues: 766.0621 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 : 2.661 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 86 THR 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 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 111 GLU 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 112 GLN 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 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 161 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 124 ASP 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 31 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR 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 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 377 ASP 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 436 VAL Chi-restraints excluded: chain H residue 444 MET 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 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 57 SER 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 K residue 438 ASN Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 514 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 58 optimal weight: 0.6980 chunk 198 optimal weight: 0.0170 chunk 240 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 171 ASN C 32 GLN C 112 GLN C 178 ASN D 154 GLN E 112 GLN F 152 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131821 restraints weight = 24510.351| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.63 r_work: 0.3246 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23250 Z= 0.183 Angle : 0.549 11.276 31763 Z= 0.289 Chirality : 0.041 0.256 3685 Planarity : 0.003 0.044 3736 Dihedral : 14.706 172.809 4236 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.82 % Allowed : 27.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2619 helix: 1.57 (0.18), residues: 888 sheet: -0.79 (0.22), residues: 474 loop : -0.79 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 473 HIS 0.003 0.001 HIS D 119 PHE 0.029 0.002 PHE K 455 TYR 0.018 0.001 TYR G 141 ARG 0.012 0.000 ARG F 25 *********************** 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: 106 poor density : 375 time to evaluate : 2.591 Fit side-chains REVERT: A 191 GLU cc_start: 0.7489 (tt0) cc_final: 0.7070 (mt-10) REVERT: B 9 TYR cc_start: 0.8816 (m-80) cc_final: 0.8428 (m-80) REVERT: B 69 ASN cc_start: 0.7607 (t0) cc_final: 0.7301 (t0) REVERT: B 72 ASP cc_start: 0.8569 (t70) cc_final: 0.8323 (t0) REVERT: C 25 ARG cc_start: 0.8278 (ttt-90) cc_final: 0.7773 (ttt180) REVERT: C 34 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: C 93 MET cc_start: 0.8429 (mmm) cc_final: 0.8156 (mmt) REVERT: C 187 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: D 3 LYS cc_start: 0.8470 (mttm) cc_final: 0.7943 (mttm) REVERT: D 12 MET cc_start: 0.9324 (ttp) cc_final: 0.9086 (ttp) REVERT: D 33 LYS cc_start: 0.8463 (mttp) cc_final: 0.7953 (mmmt) REVERT: D 123 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: E 5 MET cc_start: 0.8423 (mtm) cc_final: 0.8132 (mtp) REVERT: E 32 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: E 34 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7745 (mtm-85) REVERT: E 72 ASP cc_start: 0.8161 (t70) cc_final: 0.7875 (t70) REVERT: E 75 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: E 102 ASP cc_start: 0.8418 (m-30) cc_final: 0.8079 (t0) REVERT: E 111 GLU cc_start: 0.8557 (mp0) cc_final: 0.8212 (pm20) REVERT: E 112 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: E 170 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: F 41 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7856 (mtmt) REVERT: F 120 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8805 (mp) REVERT: F 171 ASN cc_start: 0.7611 (m110) cc_final: 0.7338 (t0) REVERT: F 187 GLU cc_start: 0.8209 (mm-30) cc_final: 0.8006 (mt-10) REVERT: F 189 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7704 (mtpm) REVERT: G 9 GLU cc_start: 0.7534 (pt0) cc_final: 0.7273 (tt0) REVERT: G 61 PHE cc_start: 0.7151 (m-80) cc_final: 0.6764 (m-80) REVERT: G 73 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7839 (pt) REVERT: G 103 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.6339 (mmm160) REVERT: G 112 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: G 188 ASP cc_start: 0.7268 (p0) cc_final: 0.6714 (p0) REVERT: H 135 GLU cc_start: 0.7941 (tt0) cc_final: 0.7694 (tt0) REVERT: H 315 SER cc_start: 0.7699 (m) cc_final: 0.7278 (m) REVERT: H 392 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7937 (ttmp) REVERT: H 418 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: H 445 CYS cc_start: 0.7790 (p) cc_final: 0.7201 (m) REVERT: H 568 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: I 476 MET cc_start: 0.6548 (ppp) cc_final: 0.5743 (tpt) REVERT: I 482 TYR cc_start: 0.6813 (t80) cc_final: 0.6119 (t80) REVERT: J 137 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: J 152 ASN cc_start: 0.8206 (t0) cc_final: 0.7833 (t0) REVERT: J 156 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7785 (mmmt) REVERT: K 440 ASN cc_start: 0.6733 (p0) cc_final: 0.6271 (p0) REVERT: L 443 ASN cc_start: 0.6032 (m-40) cc_final: 0.5358 (p0) REVERT: L 476 MET cc_start: 0.7927 (mmm) cc_final: 0.7726 (mmp) REVERT: L 518 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: L 581 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: L 600 ASN cc_start: 0.7351 (m-40) cc_final: 0.7078 (m110) outliers start: 106 outliers final: 47 residues processed: 452 average time/residue: 1.4584 time to fit residues: 748.1486 Evaluate side-chains 421 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 111 GLU 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 35 VAL 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 112 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 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 112 GLU 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 86 THR Chi-restraints excluded: chain H residue 130 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 251 VAL 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 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 514 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 171 ASN C 32 GLN C 112 GLN D 154 GLN E 112 GLN ** 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127752 restraints weight = 24319.195| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.74 r_work: 0.3172 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23250 Z= 0.303 Angle : 0.593 11.084 31763 Z= 0.309 Chirality : 0.043 0.209 3685 Planarity : 0.004 0.046 3736 Dihedral : 14.686 172.267 4236 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.63 % Allowed : 27.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2619 helix: 1.50 (0.17), residues: 894 sheet: -0.69 (0.23), residues: 445 loop : -0.83 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 125 HIS 0.005 0.001 HIS D 119 PHE 0.029 0.002 PHE H 249 TYR 0.018 0.001 TYR G 141 ARG 0.014 0.001 ARG F 25 *********************** 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 466 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 364 time to evaluate : 2.406 Fit side-chains REVERT: A 191 GLU cc_start: 0.7508 (tt0) cc_final: 0.7099 (mt-10) REVERT: B 9 TYR cc_start: 0.8863 (m-80) cc_final: 0.8631 (m-80) REVERT: B 69 ASN cc_start: 0.7674 (t0) cc_final: 0.7379 (t0) REVERT: B 72 ASP cc_start: 0.8574 (t70) cc_final: 0.8353 (t0) REVERT: C 25 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.7803 (ttt180) REVERT: C 34 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.7955 (ttp80) REVERT: C 93 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8229 (mmm) REVERT: D 3 LYS cc_start: 0.8471 (mttm) cc_final: 0.7821 (mtpt) REVERT: D 34 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7740 (ttm110) REVERT: D 123 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: E 5 MET cc_start: 0.8356 (mtm) cc_final: 0.8100 (mtp) REVERT: E 32 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: E 72 ASP cc_start: 0.8124 (t70) cc_final: 0.7874 (t70) REVERT: E 75 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: E 102 ASP cc_start: 0.8432 (m-30) cc_final: 0.7978 (t0) REVERT: E 111 GLU cc_start: 0.8610 (mp0) cc_final: 0.8202 (pm20) REVERT: E 112 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: E 170 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8417 (pt0) REVERT: F 41 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7922 (mtmt) REVERT: F 98 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7783 (ttp-170) REVERT: F 120 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8830 (mp) REVERT: F 171 ASN cc_start: 0.7706 (m110) cc_final: 0.7442 (t0) REVERT: F 189 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7732 (mtpm) REVERT: G 9 GLU cc_start: 0.7582 (pt0) cc_final: 0.7296 (tt0) REVERT: G 61 PHE cc_start: 0.7192 (m-80) cc_final: 0.6828 (m-80) REVERT: G 73 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7845 (pt) REVERT: G 103 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.6415 (mmm160) REVERT: G 109 GLU cc_start: 0.8364 (pt0) cc_final: 0.8122 (pt0) REVERT: G 112 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: G 116 TYR cc_start: 0.8868 (m-80) cc_final: 0.8614 (m-80) REVERT: G 188 ASP cc_start: 0.7157 (p0) cc_final: 0.6669 (p0) REVERT: H 54 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7610 (mttm) REVERT: H 135 GLU cc_start: 0.7932 (tt0) cc_final: 0.7684 (tt0) REVERT: H 315 SER cc_start: 0.7884 (m) cc_final: 0.7477 (m) REVERT: H 392 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7989 (ttmm) REVERT: H 418 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: H 445 CYS cc_start: 0.7754 (p) cc_final: 0.7290 (m) REVERT: H 475 ASP cc_start: 0.6739 (m-30) cc_final: 0.6110 (t0) REVERT: H 568 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: I 476 MET cc_start: 0.6640 (ppp) cc_final: 0.5970 (tpt) REVERT: I 477 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6240 (mp) REVERT: I 515 GLU cc_start: 0.8562 (tt0) cc_final: 0.8296 (tt0) REVERT: J 62 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8796 (mtp) REVERT: J 137 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: J 152 ASN cc_start: 0.8197 (t0) cc_final: 0.7814 (t0) REVERT: J 154 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: J 187 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: K 440 ASN cc_start: 0.6828 (p0) cc_final: 0.6418 (p0) REVERT: K 595 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6312 (tttm) REVERT: L 443 ASN cc_start: 0.6012 (m-40) cc_final: 0.5360 (p0) REVERT: L 476 MET cc_start: 0.7976 (mmm) cc_final: 0.7772 (mmp) REVERT: L 518 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: L 581 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: L 600 ASN cc_start: 0.7352 (m-40) cc_final: 0.7052 (m110) outliers start: 102 outliers final: 55 residues processed: 435 average time/residue: 1.4678 time to fit residues: 725.2424 Evaluate side-chains 432 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 355 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 111 GLU 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 35 VAL 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 112 GLN Chi-restraints excluded: chain E residue 150 ILE 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 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR 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 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 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 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 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 57 SER Chi-restraints excluded: chain J residue 62 MET 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 187 GLU 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 472 ASN Chi-restraints excluded: chain L residue 514 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 287 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128101 restraints weight = 24607.591| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.70 r_work: 0.3193 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23250 Z= 0.257 Angle : 0.579 11.052 31763 Z= 0.302 Chirality : 0.042 0.223 3685 Planarity : 0.004 0.049 3736 Dihedral : 14.685 172.624 4236 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.86 % Allowed : 28.08 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2619 helix: 1.64 (0.18), residues: 883 sheet: -0.73 (0.23), residues: 455 loop : -0.74 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 564 HIS 0.004 0.001 HIS D 119 PHE 0.030 0.002 PHE H 249 TYR 0.022 0.001 TYR G 141 ARG 0.014 0.001 ARG F 25 *********************** 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 447 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 362 time to evaluate : 2.508 Fit side-chains REVERT: A 191 GLU cc_start: 0.7510 (tt0) cc_final: 0.7098 (mt-10) REVERT: B 9 TYR cc_start: 0.8864 (m-80) cc_final: 0.8628 (m-80) REVERT: B 69 ASN cc_start: 0.7672 (t0) cc_final: 0.7378 (t0) REVERT: B 93 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8193 (tpt) REVERT: C 25 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.7815 (ttt180) REVERT: C 34 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7953 (ttp80) REVERT: C 93 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: C 187 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: D 3 LYS cc_start: 0.8509 (mttm) cc_final: 0.7868 (mtpt) REVERT: D 12 MET cc_start: 0.9318 (ttp) cc_final: 0.9060 (ttp) REVERT: D 34 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7721 (ttm110) REVERT: D 123 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: E 5 MET cc_start: 0.8364 (mtm) cc_final: 0.8121 (mtp) REVERT: E 32 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: E 72 ASP cc_start: 0.8145 (t70) cc_final: 0.7882 (t70) REVERT: E 75 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: E 102 ASP cc_start: 0.8438 (m-30) cc_final: 0.8074 (t0) REVERT: E 111 GLU cc_start: 0.8630 (mp0) cc_final: 0.8304 (pm20) REVERT: E 112 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: E 170 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: F 41 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8006 (mtmt) REVERT: F 98 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7607 (ttp-170) REVERT: F 120 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8819 (mp) REVERT: F 171 ASN cc_start: 0.7699 (m110) cc_final: 0.7466 (t0) REVERT: F 189 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7716 (mtpm) REVERT: G 9 GLU cc_start: 0.7599 (pt0) cc_final: 0.7338 (tt0) REVERT: G 61 PHE cc_start: 0.7285 (m-80) cc_final: 0.6924 (m-80) REVERT: G 73 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7848 (pt) REVERT: G 103 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.6409 (mmm160) REVERT: G 109 GLU cc_start: 0.8396 (pt0) cc_final: 0.8184 (pt0) REVERT: G 112 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: G 116 TYR cc_start: 0.8850 (m-80) cc_final: 0.8601 (m-80) REVERT: G 188 ASP cc_start: 0.7146 (p0) cc_final: 0.6670 (p0) REVERT: H 54 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7908 (mmtm) REVERT: H 135 GLU cc_start: 0.7917 (tt0) cc_final: 0.7695 (tt0) REVERT: H 315 SER cc_start: 0.7799 (m) cc_final: 0.7242 (m) REVERT: H 392 LYS cc_start: 0.8245 (ttmt) cc_final: 0.8017 (ttmm) REVERT: H 418 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: H 445 CYS cc_start: 0.7751 (p) cc_final: 0.7259 (m) REVERT: H 475 ASP cc_start: 0.6715 (m-30) cc_final: 0.6117 (t0) REVERT: H 568 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: I 476 MET cc_start: 0.6736 (ppp) cc_final: 0.6071 (tpt) REVERT: I 477 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6244 (mp) REVERT: I 515 GLU cc_start: 0.8568 (tt0) cc_final: 0.8300 (tt0) REVERT: J 62 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: J 137 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: J 152 ASN cc_start: 0.8213 (t0) cc_final: 0.7827 (t0) REVERT: J 154 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: J 187 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: K 440 ASN cc_start: 0.6840 (p0) cc_final: 0.6453 (p0) REVERT: K 595 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6312 (tttm) REVERT: L 443 ASN cc_start: 0.5950 (m-40) cc_final: 0.5338 (p0) REVERT: L 476 MET cc_start: 0.8034 (mmm) cc_final: 0.7815 (mmp) REVERT: L 518 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: L 581 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: L 600 ASN cc_start: 0.7354 (m-40) cc_final: 0.7047 (m110) outliers start: 85 outliers final: 49 residues processed: 422 average time/residue: 1.4712 time to fit residues: 704.8017 Evaluate side-chains 436 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 363 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 93 MET 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 111 GLU 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 D residue 192 ASP Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 35 VAL 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 112 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 120 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR 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 251 VAL 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 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 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 57 SER Chi-restraints excluded: chain J residue 62 MET 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 187 GLU 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 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 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 171 ASN C 32 GLN D 154 GLN ** G 147 ASN ** 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 K 488 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128629 restraints weight = 24502.953| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.65 r_work: 0.3196 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23250 Z= 0.260 Angle : 0.580 10.977 31763 Z= 0.302 Chirality : 0.042 0.223 3685 Planarity : 0.004 0.051 3736 Dihedral : 14.648 172.860 4236 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.86 % Allowed : 28.08 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2619 helix: 1.63 (0.17), residues: 893 sheet: -0.73 (0.22), residues: 480 loop : -0.81 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 564 HIS 0.005 0.001 HIS D 119 PHE 0.033 0.002 PHE H 249 TYR 0.012 0.001 TYR G 137 ARG 0.015 0.001 ARG F 25 ********************** 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 446 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 361 time to evaluate : 2.528 Fit side-chains REVERT: B 69 ASN cc_start: 0.7678 (t0) cc_final: 0.7408 (t0) REVERT: B 93 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8171 (tpt) REVERT: C 25 ARG cc_start: 0.8311 (ttt-90) cc_final: 0.7805 (ttt180) REVERT: C 34 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7951 (ttp80) REVERT: C 93 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: C 187 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7612 (pp20) REVERT: D 3 LYS cc_start: 0.8544 (mttm) cc_final: 0.7980 (mttm) REVERT: D 12 MET cc_start: 0.9330 (ttp) cc_final: 0.9055 (ttp) REVERT: D 34 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7704 (ttm110) REVERT: D 123 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: E 5 MET cc_start: 0.8361 (mtm) cc_final: 0.8096 (mtp) REVERT: E 32 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: E 75 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: E 102 ASP cc_start: 0.8436 (m-30) cc_final: 0.8077 (t0) REVERT: E 111 GLU cc_start: 0.8621 (mp0) cc_final: 0.8261 (pm20) REVERT: E 112 GLN cc_start: 0.8469 (mp10) cc_final: 0.8106 (mt0) REVERT: E 170 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: F 41 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7995 (mtmt) REVERT: F 98 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7629 (ttp-170) REVERT: F 120 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8825 (mp) REVERT: F 189 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7762 (mtpm) REVERT: G 9 GLU cc_start: 0.7555 (pt0) cc_final: 0.7306 (tt0) REVERT: G 61 PHE cc_start: 0.7268 (m-80) cc_final: 0.6927 (m-80) REVERT: G 103 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6422 (mmm160) REVERT: G 116 TYR cc_start: 0.8896 (m-80) cc_final: 0.8661 (m-80) REVERT: G 188 ASP cc_start: 0.7115 (p0) cc_final: 0.6675 (p0) REVERT: H 54 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (mmtm) REVERT: H 135 GLU cc_start: 0.7881 (tt0) cc_final: 0.7652 (tt0) REVERT: H 315 SER cc_start: 0.7789 (m) cc_final: 0.7289 (m) REVERT: H 392 LYS cc_start: 0.8253 (ttmt) cc_final: 0.8040 (ttmm) REVERT: H 418 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: H 445 CYS cc_start: 0.7810 (p) cc_final: 0.7185 (m) REVERT: H 475 ASP cc_start: 0.6705 (m-30) cc_final: 0.6123 (t0) REVERT: H 568 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: I 476 MET cc_start: 0.6753 (ppp) cc_final: 0.5892 (tpt) REVERT: I 477 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6245 (mp) REVERT: I 515 GLU cc_start: 0.8564 (tt0) cc_final: 0.8291 (tt0) REVERT: J 62 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8766 (mtp) REVERT: J 137 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: J 152 ASN cc_start: 0.8169 (t0) cc_final: 0.7814 (t0) REVERT: J 154 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: J 187 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: K 440 ASN cc_start: 0.6848 (p0) cc_final: 0.6463 (p0) REVERT: K 595 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6340 (tttm) REVERT: L 443 ASN cc_start: 0.5955 (m-40) cc_final: 0.5324 (p0) REVERT: L 476 MET cc_start: 0.8038 (mmm) cc_final: 0.7814 (mmp) REVERT: L 518 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: L 581 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: L 600 ASN cc_start: 0.7334 (m-40) cc_final: 0.7039 (m110) outliers start: 85 outliers final: 52 residues processed: 423 average time/residue: 1.5197 time to fit residues: 728.6201 Evaluate side-chains 420 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 347 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 MET 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 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 111 GLU 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 35 VAL 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 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 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR 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 251 VAL 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 323 ILE 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 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 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 57 SER Chi-restraints excluded: chain J residue 62 MET 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 187 GLU 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 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 20 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 171 ASN C 32 GLN C 178 ASN D 154 GLN F 171 ASN ** G 147 ASN ** 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 I 558 ASN J 45 ASN K 488 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127015 restraints weight = 24389.481| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.77 r_work: 0.3159 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23250 Z= 0.325 Angle : 0.614 11.180 31763 Z= 0.319 Chirality : 0.043 0.212 3685 Planarity : 0.004 0.048 3736 Dihedral : 14.645 171.991 4236 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2619 helix: 1.56 (0.17), residues: 893 sheet: -0.68 (0.23), residues: 460 loop : -0.79 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.006 0.001 HIS D 119 PHE 0.033 0.002 PHE H 249 TYR 0.021 0.001 TYR G 141 ARG 0.014 0.001 ARG F 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16828.06 seconds wall clock time: 300 minutes 22.47 seconds (18022.47 seconds total)