Starting phenix.real_space_refine on Fri Sep 19 02:35:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4l_39767/09_2025/8z4l_39767_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4l_39767/09_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_39767/09_2025/8z4l_39767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4l_39767/09_2025/8z4l_39767.map" model { file = "/net/cci-nas-00/data/ceres_data/8z4l_39767/09_2025/8z4l_39767_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4l_39767/09_2025/8z4l_39767_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 89 5.49 5 S 94 5.16 5 C 14033 2.51 5 N 3946 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1107 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1523 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1598 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "H" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4394 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 18, 'TRANS': 537} Chain breaks: 8 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 105 Chain: "I" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1349 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1917 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 7 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1303 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1023 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna2p': 24, 'rna3p': 24} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 857 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 33} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 359 SG CYS A 71 34.531 52.114 183.826 1.00 87.92 S ATOM 433 SG CYS A 81 33.656 51.667 182.434 1.00 78.21 S ATOM 448 SG CYS A 84 33.153 53.602 185.366 1.00 77.01 S ATOM 1655 SG CYS B 71 25.897 75.698 161.117 1.00 74.95 S ATOM 1729 SG CYS B 81 24.208 77.838 159.183 1.00 62.73 S ATOM 1750 SG CYS B 84 26.696 79.340 162.223 1.00 47.13 S ATOM 1770 SG CYS B 87 28.131 78.376 159.428 1.00 57.73 S ATOM 3182 SG CYS C 71 39.730 95.189 136.748 1.00 52.93 S ATOM 3256 SG CYS C 81 39.924 98.277 134.430 1.00 40.13 S ATOM 3277 SG CYS C 84 42.543 97.839 137.250 1.00 34.48 S ATOM 3297 SG CYS C 87 42.610 95.531 134.523 1.00 39.41 S ATOM 4725 SG CYS D 71 75.939 74.109 87.574 1.00 48.86 S ATOM 4799 SG CYS D 81 78.474 72.613 84.786 1.00 54.41 S ATOM 4820 SG CYS D 84 78.261 71.547 87.704 1.00 63.81 S ATOM 4840 SG CYS D 87 75.086 70.678 85.952 1.00 27.80 S ATOM 6268 SG CYS E 71 66.669 49.901 65.552 1.00 69.72 S ATOM 6342 SG CYS E 81 67.288 47.024 63.026 1.00 58.53 S ATOM 6363 SG CYS E 84 66.304 46.173 65.693 1.00 79.57 S ATOM 6383 SG CYS E 87 63.596 48.497 63.831 1.00 38.76 S ATOM 7792 SG CYS F 71 41.766 40.600 43.219 1.00 79.22 S ATOM 7856 SG CYS F 81 39.256 40.217 41.495 1.00 87.00 S ATOM 7871 SG CYS F 84 38.173 41.174 45.185 1.00 79.01 S ATOM 7891 SG CYS F 87 39.183 43.744 43.021 1.00 78.88 S ATOM 9235 SG CYS G 70 36.845 91.984 36.316 1.00 94.28 S ATOM 9340 SG CYS G 85 38.577 88.971 33.712 1.00 98.77 S ATOM 9359 SG CYS G 88 39.935 92.422 35.811 1.00 95.30 S ATOM 16609 SG CYS J 71 62.852 94.205 111.637 1.00 48.54 S ATOM 16683 SG CYS J 81 65.418 95.835 109.218 1.00 44.99 S ATOM 16704 SG CYS J 84 66.660 93.693 112.099 1.00 44.79 S ATOM 16724 SG CYS J 87 64.685 92.036 109.403 1.00 30.99 S Time building chain proxies: 4.91, per 1000 atoms: 0.22 Number of scatterers: 22713 At special positions: 0 Unit cell: (93.1, 119.7, 217.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 94 16.00 P 89 15.00 O 4542 8.00 N 3946 7.00 C 14033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " Number of angles added : 36 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5042 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 35 sheets defined 35.9% alpha, 20.9% beta 21 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.808A pdb=" N LYS A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 155 through 172 removed outlier: 4.577A pdb=" N SER A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.566A pdb=" N GLY C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.656A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 removed outlier: 3.553A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.612A pdb=" N GLY E 180 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.571A pdb=" N TYR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.920A pdb=" N LYS G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 124 through 141 removed outlier: 3.702A pdb=" N ASN G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 64 through 69 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 107 removed outlier: 3.709A pdb=" N GLU H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.539A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 274 through 278 removed outlier: 3.649A pdb=" N ARG H 278 " --> pdb=" O LYS H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 323 through 332 removed outlier: 4.147A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 330 " --> pdb=" O HIS H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 355 Processing helix chain 'H' and resid 375 through 384 Processing helix chain 'H' and resid 399 through 412 removed outlier: 3.681A pdb=" N GLU H 404 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 482 removed outlier: 3.546A pdb=" N PHE H 474 " --> pdb=" O ASP H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 539 Processing helix chain 'H' and resid 542 through 554 Processing helix chain 'H' and resid 572 through 593 removed outlier: 3.742A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR H 593 " --> pdb=" O SER H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 604 removed outlier: 3.988A pdb=" N ASN H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE H 601 " --> pdb=" O LYS H 597 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN H 604 " --> pdb=" O ASN H 600 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 488 removed outlier: 3.582A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG I 486 " --> pdb=" O TYR I 482 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 593 removed outlier: 4.140A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR I 593 " --> pdb=" O SER I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 604 removed outlier: 3.929A pdb=" N ASN I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 154 through 157 removed outlier: 3.739A pdb=" N ASP J 157 " --> pdb=" O GLN J 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 154 through 157' Processing helix chain 'J' and resid 158 through 172 Processing helix chain 'K' and resid 378 through 386 removed outlier: 3.600A pdb=" N TYR K 382 " --> pdb=" O GLU K 378 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 386 " --> pdb=" O TYR K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'K' and resid 470 through 487 removed outlier: 3.579A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS K 484 " --> pdb=" O GLU K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 Processing helix chain 'K' and resid 541 through 554 removed outlier: 3.598A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 592 removed outlier: 4.026A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 488 removed outlier: 3.555A pdb=" N PHE L 474 " --> pdb=" O ASP L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 523 Processing helix chain 'L' and resid 527 through 540 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 572 through 590 Processing helix chain 'L' and resid 594 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.610A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 122 removed outlier: 3.848A pdb=" N ASP B 131 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.400A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.380A pdb=" N ARG E 115 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU E 136 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER E 117 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS E 119 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR E 132 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG E 121 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 99 through 101 removed outlier: 3.893A pdb=" N MET F 5 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 193 " --> pdb=" O MET F 5 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 122 removed outlier: 6.579A pdb=" N ARG F 115 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU F 136 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER F 117 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 119 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR F 132 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG F 121 " --> pdb=" O SER F 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC3, first strand: chain 'G' and resid 214 through 216 Processing sheet with id=AC4, first strand: chain 'G' and resid 189 through 190 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 5 removed outlier: 6.741A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE H 25 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS H 24 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE H 59 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU H 26 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP H 56 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 140 through 145 removed outlier: 8.743A pdb=" N VAL H 153 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY H 168 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN H 163 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE H 193 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU H 165 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 225 through 228 removed outlier: 6.633A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE H 227 " --> pdb=" O SER H 313 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.642A pdb=" N GLU H 365 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 434 through 436 Processing sheet with id=AD1, first strand: chain 'H' and resid 434 through 436 removed outlier: 4.732A pdb=" N ARG H 451 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG K 451 " --> pdb=" O GLU H 461 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 445 through 447 Processing sheet with id=AD3, first strand: chain 'I' and resid 467 through 469 Processing sheet with id=AD4, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD5, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD6, first strand: chain 'J' and resid 114 through 122 removed outlier: 6.402A pdb=" N ARG J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU J 136 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER J 117 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 134 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.854A pdb=" N GLY K 162 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN K 163 " --> pdb=" O TYR K 191 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE K 193 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU K 165 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 445 through 447 910 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 2.39 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 301)) selection = (chain 'J' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 through 82 or (resid 83 and \ (name N or name CA or name C or name O or name CB )) or resid 84 through 94 or ( \ resid 95 through 96 and (name N or name CA or name C or name O or name CB )) or \ resid 97 through 110 or (resid 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or resid 126 through 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 186 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 196 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 479 or (resid \ 480 and (name N or name CA or name C or name O or name CB )) or resid 481 throug \ h 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) or \ resid 486 through 487 or (resid 488 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 569 or (resid 570 and (name N \ or name CA or name C or name O or name CB )) or resid 571 through 577 or (resid \ 578 and (name N or name CA or name C or name O or name CB )) or resid 579 throug \ h 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) or \ resid 593 through 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB )) or resid 598 through 607 or (resid 608 through 609 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 436 through 466 or (resid 467 and (name N or name CA or name C or n \ ame O or name CB )) or resid 468 through 609)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.340 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- 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 0.162 23283 Z= 0.447 Angle : 1.296 29.539 31799 Z= 0.735 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.14), residues: 2619 helix: -1.50 (0.15), residues: 843 sheet: -1.69 (0.21), residues: 488 loop : -1.99 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 79 TYR 0.031 0.003 TYR F 19 PHE 0.060 0.005 PHE G 41 TRP 0.031 0.003 TRP I 535 HIS 0.028 0.005 HIS L 510 Details of bonding type rmsd covalent geometry : bond 0.00763 (23250) covalent geometry : angle 1.23413 (31763) hydrogen bonds : bond 0.15965 ( 930) hydrogen bonds : angle 7.98425 ( 2717) metal coordination : bond 0.03762 ( 33) metal coordination : angle 11.80309 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 486 time to evaluate : 0.853 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: 0.6713 time to fit residues: 384.7708 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 : 0.726 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 119 HIS B 154 GLN B 178 ASN C 32 GLN C 36 ASN C 154 GLN C 178 ASN E 112 GLN F 171 ASN G 99 ASN G 147 ASN H 50 ASN H 81 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN H 397 HIS ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN I 558 ASN J 45 ASN J 112 GLN K 443 ASN K 446 ASN K 606 ASN L 510 HIS L 516 ASN L 556 ASN L 596 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129342 restraints weight = 24677.892| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.03 r_work: 0.3161 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23283 Z= 0.280 Angle : 0.786 24.336 31799 Z= 0.382 Chirality : 0.046 0.214 3685 Planarity : 0.005 0.064 3736 Dihedral : 15.088 166.362 4261 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 7.13 % Allowed : 22.67 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.15), residues: 2619 helix: -0.04 (0.16), residues: 875 sheet: -1.12 (0.23), residues: 445 loop : -1.47 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 56 TYR 0.036 0.002 TYR H 245 PHE 0.027 0.003 PHE C 103 TRP 0.016 0.002 TRP H 125 HIS 0.009 0.002 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00642 (23250) covalent geometry : angle 0.71331 (31763) hydrogen bonds : bond 0.04586 ( 930) hydrogen bonds : angle 5.58517 ( 2717) metal coordination : bond 0.01185 ( 33) metal coordination : angle 9.85394 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 420 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7041 (t) REVERT: A 156 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6480 (mmtt) REVERT: A 191 GLU cc_start: 0.6924 (tt0) cc_final: 0.6543 (mt-10) REVERT: A 198 PHE cc_start: 0.7873 (m-80) cc_final: 0.7627 (m-80) REVERT: B 64 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7928 (tttm) REVERT: B 69 ASN cc_start: 0.7759 (t0) cc_final: 0.7454 (t0) REVERT: B 72 ASP cc_start: 0.8351 (t0) cc_final: 0.7890 (t70) REVERT: B 179 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8654 (ttmt) REVERT: C 25 ARG cc_start: 0.8361 (ttt-90) cc_final: 0.7954 (ttp80) REVERT: C 34 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.7894 (ttp80) REVERT: C 93 MET cc_start: 0.8650 (mmm) cc_final: 0.8386 (mmm) REVERT: C 111 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: D 34 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7737 (ttm110) REVERT: D 123 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: D 131 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (m-30) REVERT: D 189 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8488 (mptm) REVERT: E 72 ASP cc_start: 0.8210 (t70) cc_final: 0.7735 (t70) REVERT: E 75 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: E 83 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7690 (mpp-170) REVERT: E 102 ASP cc_start: 0.8561 (m-30) cc_final: 0.8106 (t0) REVERT: E 112 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: E 190 SER cc_start: 0.8962 (p) cc_final: 0.8722 (m) REVERT: E 191 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: E 197 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7496 (ptt90) REVERT: F 92 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7847 (t) REVERT: F 137 GLU cc_start: 0.8253 (pt0) cc_final: 0.7980 (pt0) REVERT: F 187 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: G 26 TYR cc_start: 0.6889 (p90) cc_final: 0.6252 (p90) REVERT: G 98 ARG cc_start: 0.8451 (mmt-90) cc_final: 0.8247 (mmt-90) REVERT: G 103 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.6375 (mmm160) REVERT: G 116 TYR cc_start: 0.8835 (m-80) cc_final: 0.8440 (m-80) REVERT: H 56 ASP cc_start: 0.7410 (t0) cc_final: 0.7140 (t0) REVERT: H 91 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: H 135 GLU cc_start: 0.7945 (tt0) cc_final: 0.7688 (tt0) REVERT: H 178 MET cc_start: 0.7555 (mpt) cc_final: 0.7283 (mtm) REVERT: H 277 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6876 (ttp-170) REVERT: H 287 ASN cc_start: 0.7458 (t0) cc_final: 0.7176 (t0) REVERT: H 392 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7912 (ttmm) REVERT: H 568 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: I 482 TYR cc_start: 0.6896 (t80) cc_final: 0.6159 (t80) REVERT: I 559 THR cc_start: 0.8899 (p) cc_final: 0.8644 (p) REVERT: J 33 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8130 (mmtm) REVERT: J 123 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: J 137 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: J 152 ASN cc_start: 0.8457 (t0) cc_final: 0.7860 (t0) REVERT: J 154 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: J 197 ARG cc_start: 0.8525 (ptt90) cc_final: 0.8170 (ptt180) REVERT: K 161 ASN cc_start: 0.7705 (t0) cc_final: 0.6894 (p0) REVERT: K 444 MET cc_start: 0.7316 (mtm) cc_final: 0.6874 (mpp) REVERT: K 455 PHE cc_start: 0.7351 (t80) cc_final: 0.7123 (t80) REVERT: K 459 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7813 (pt) REVERT: K 518 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: K 554 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7472 (ttp-110) REVERT: L 443 ASN cc_start: 0.6195 (m-40) cc_final: 0.5250 (p0) REVERT: L 551 GLN cc_start: 0.7858 (tt0) cc_final: 0.7517 (tt0) REVERT: L 581 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: L 600 ASN cc_start: 0.7345 (m-40) cc_final: 0.6933 (m110) outliers start: 157 outliers final: 49 residues processed: 532 average time/residue: 0.6195 time to fit residues: 374.0295 Evaluate side-chains 440 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 76 SER 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 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 191 GLU 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 140 SER Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 155 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 518 GLU Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 124 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 45 ASN C 178 ASN D 112 GLN D 154 GLN F 152 ASN G 99 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 551 GLN I 483 ASN J 32 GLN J 45 ASN K 438 ASN K 443 ASN K 522 ASN L 446 ASN L 510 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126984 restraints weight = 24416.056| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.68 r_work: 0.3163 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23283 Z= 0.250 Angle : 0.718 24.470 31799 Z= 0.347 Chirality : 0.044 0.211 3685 Planarity : 0.005 0.051 3736 Dihedral : 14.925 167.347 4237 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.68 % Allowed : 23.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 2619 helix: 0.51 (0.17), residues: 894 sheet: -0.87 (0.23), residues: 435 loop : -1.34 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 25 TYR 0.023 0.001 TYR H 245 PHE 0.023 0.002 PHE C 103 TRP 0.011 0.002 TRP H 564 HIS 0.007 0.002 HIS L 510 Details of bonding type rmsd covalent geometry : bond 0.00569 (23250) covalent geometry : angle 0.64853 (31763) hydrogen bonds : bond 0.04210 ( 930) hydrogen bonds : angle 5.22324 ( 2717) metal coordination : bond 0.01366 ( 33) metal coordination : angle 9.21431 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 385 time to evaluate : 0.812 Fit side-chains REVERT: A 156 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6577 (mmtt) REVERT: A 191 GLU cc_start: 0.7213 (tt0) cc_final: 0.6780 (mt-10) REVERT: B 9 TYR cc_start: 0.8847 (m-80) cc_final: 0.8555 (m-80) REVERT: B 64 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8021 (tttm) REVERT: B 69 ASN cc_start: 0.7854 (t0) cc_final: 0.7639 (t0) REVERT: C 25 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7817 (ttt180) REVERT: C 34 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8112 (ttp80) REVERT: C 93 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: C 154 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: D 34 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7723 (ttm110) REVERT: D 123 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: D 189 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8540 (mptm) REVERT: D 192 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: E 32 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: E 72 ASP cc_start: 0.8205 (t70) cc_final: 0.7846 (t70) REVERT: E 75 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: E 83 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7466 (mpp-170) REVERT: E 102 ASP cc_start: 0.8495 (m-30) cc_final: 0.8101 (t0) REVERT: E 112 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: E 154 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: E 170 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: F 41 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8011 (mtmt) REVERT: F 64 LYS cc_start: 0.8398 (tttp) cc_final: 0.8144 (tttt) REVERT: F 92 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7880 (t) REVERT: F 152 ASN cc_start: 0.7517 (t0) cc_final: 0.7164 (t0) REVERT: F 187 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: G 9 GLU cc_start: 0.7588 (pt0) cc_final: 0.7159 (tt0) REVERT: G 26 TYR cc_start: 0.6959 (p90) cc_final: 0.6673 (p90) REVERT: G 55 ASP cc_start: 0.6082 (m-30) cc_final: 0.5320 (t70) REVERT: G 61 PHE cc_start: 0.6946 (m-80) cc_final: 0.6545 (m-80) REVERT: G 98 ARG cc_start: 0.8515 (mmt-90) cc_final: 0.8290 (mmt90) REVERT: G 103 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.6385 (mmm160) REVERT: H 56 ASP cc_start: 0.7462 (t0) cc_final: 0.7241 (t0) REVERT: H 91 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: H 127 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: H 135 GLU cc_start: 0.8088 (tt0) cc_final: 0.7758 (tt0) REVERT: H 178 MET cc_start: 0.7632 (mpt) cc_final: 0.7313 (mtm) REVERT: H 277 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6770 (mtm180) REVERT: H 287 ASN cc_start: 0.7416 (t0) cc_final: 0.7146 (t0) REVERT: H 315 SER cc_start: 0.8222 (p) cc_final: 0.7724 (t) REVERT: H 392 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7897 (ttmp) REVERT: H 418 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6698 (tm-30) REVERT: H 432 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: H 461 GLU cc_start: 0.7063 (tt0) cc_final: 0.6481 (mt-10) REVERT: H 568 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: J 33 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8215 (mmtm) REVERT: J 123 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: J 137 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: J 152 ASN cc_start: 0.8358 (t0) cc_final: 0.7748 (t0) REVERT: J 154 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: K 161 ASN cc_start: 0.7717 (t0) cc_final: 0.6885 (p0) REVERT: K 518 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: L 443 ASN cc_start: 0.6031 (m-40) cc_final: 0.5095 (p0) REVERT: L 551 GLN cc_start: 0.7823 (tt0) cc_final: 0.7587 (tt0) REVERT: L 581 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: L 600 ASN cc_start: 0.7360 (m-40) cc_final: 0.7066 (m110) outliers start: 147 outliers final: 54 residues processed: 492 average time/residue: 0.6078 time to fit residues: 339.5050 Evaluate side-chains 436 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 356 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 93 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 LYS 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 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 92 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 124 ASP 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 31 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 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 410 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 515 GLU Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 378 GLU Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 446 ASN Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 581 GLU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 199 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 C 32 GLN C 112 GLN C 178 ASN D 154 GLN D 171 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 45 ASN K 438 ASN K 443 ASN K 446 ASN L 510 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127470 restraints weight = 24427.201| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.63 r_work: 0.3179 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23283 Z= 0.207 Angle : 0.662 22.923 31799 Z= 0.321 Chirality : 0.043 0.211 3685 Planarity : 0.004 0.041 3736 Dihedral : 14.841 168.563 4236 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.45 % Allowed : 24.85 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.16), residues: 2619 helix: 0.88 (0.17), residues: 894 sheet: -0.85 (0.22), residues: 447 loop : -1.15 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 25 TYR 0.019 0.001 TYR H 245 PHE 0.023 0.002 PHE K 455 TRP 0.010 0.001 TRP H 564 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00474 (23250) covalent geometry : angle 0.60119 (31763) hydrogen bonds : bond 0.03846 ( 930) hydrogen bonds : angle 5.04370 ( 2717) metal coordination : bond 0.00953 ( 33) metal coordination : angle 8.27634 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 387 time to evaluate : 0.665 Fit side-chains REVERT: A 191 GLU cc_start: 0.7290 (tt0) cc_final: 0.6854 (mt-10) REVERT: B 9 TYR cc_start: 0.8959 (m-80) cc_final: 0.8571 (m-80) REVERT: B 64 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: B 69 ASN cc_start: 0.8018 (t0) cc_final: 0.7761 (t0) REVERT: C 25 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.7998 (ttt180) REVERT: C 34 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.8170 (ttp80) REVERT: C 93 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8316 (mmm) REVERT: C 154 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: D 3 LYS cc_start: 0.8501 (mttm) cc_final: 0.7786 (mtpt) REVERT: D 34 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7910 (ttm110) REVERT: D 123 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: D 192 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: E 32 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: E 72 ASP cc_start: 0.8325 (t70) cc_final: 0.7880 (t70) REVERT: E 75 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: E 83 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7755 (mpp-170) REVERT: E 102 ASP cc_start: 0.8664 (m-30) cc_final: 0.8229 (t0) REVERT: E 112 GLN cc_start: 0.8624 (mp10) cc_final: 0.8384 (mt0) REVERT: E 154 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: E 170 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: F 41 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8007 (mtmt) REVERT: F 92 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7924 (t) REVERT: F 171 ASN cc_start: 0.7747 (m110) cc_final: 0.7463 (t0) REVERT: F 187 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: G 9 GLU cc_start: 0.7633 (pt0) cc_final: 0.7209 (tt0) REVERT: G 55 ASP cc_start: 0.6055 (m-30) cc_final: 0.5294 (t70) REVERT: G 61 PHE cc_start: 0.6991 (m-80) cc_final: 0.6566 (m-80) REVERT: G 103 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.6397 (mmm160) REVERT: G 116 TYR cc_start: 0.8693 (m-80) cc_final: 0.8424 (m-80) REVERT: H 56 ASP cc_start: 0.7753 (t0) cc_final: 0.7547 (t0) REVERT: H 91 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: H 127 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: H 135 GLU cc_start: 0.8272 (tt0) cc_final: 0.8040 (tt0) REVERT: H 178 MET cc_start: 0.7815 (mpt) cc_final: 0.7494 (mtm) REVERT: H 287 ASN cc_start: 0.7593 (t0) cc_final: 0.7290 (t0) REVERT: H 315 SER cc_start: 0.8306 (p) cc_final: 0.7777 (t) REVERT: H 392 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8108 (ttmp) REVERT: H 418 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: H 445 CYS cc_start: 0.7953 (p) cc_final: 0.7577 (m) REVERT: H 453 MET cc_start: 0.8850 (ptm) cc_final: 0.8580 (ptm) REVERT: H 461 GLU cc_start: 0.7170 (tt0) cc_final: 0.6589 (mt-10) REVERT: H 536 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8164 (mt-10) REVERT: H 568 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: I 446 ASN cc_start: 0.6881 (p0) cc_final: 0.6288 (p0) REVERT: I 577 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: I 594 ASP cc_start: 0.8539 (p0) cc_final: 0.8314 (p0) REVERT: J 33 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8246 (mmtm) REVERT: J 123 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: J 137 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: J 152 ASN cc_start: 0.8417 (t0) cc_final: 0.7851 (t0) REVERT: K 161 ASN cc_start: 0.7683 (t0) cc_final: 0.6858 (p0) REVERT: K 518 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: K 554 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7463 (ttm110) REVERT: L 443 ASN cc_start: 0.6048 (m-40) cc_final: 0.5291 (p0) REVERT: L 470 ASP cc_start: 0.8002 (p0) cc_final: 0.7797 (p0) REVERT: L 476 MET cc_start: 0.8161 (mmm) cc_final: 0.7952 (mmp) REVERT: L 551 GLN cc_start: 0.7933 (tt0) cc_final: 0.7649 (tt0) REVERT: L 581 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: L 600 ASN cc_start: 0.7431 (m-40) cc_final: 0.7102 (m110) outliers start: 142 outliers final: 58 residues processed: 490 average time/residue: 0.6418 time to fit residues: 355.4030 Evaluate side-chains 444 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 363 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 70 VAL 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 154 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 191 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 147 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 418 GLU 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 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 470 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 554 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 186 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 C 32 GLN C 112 GLN C 178 ASN D 154 GLN F 152 ASN G 99 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN K 438 ASN L 446 ASN L 510 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126963 restraints weight = 24462.984| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.75 r_work: 0.3169 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23283 Z= 0.203 Angle : 0.648 22.420 31799 Z= 0.315 Chirality : 0.043 0.211 3685 Planarity : 0.004 0.044 3736 Dihedral : 14.799 169.107 4236 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.00 % Allowed : 25.72 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2619 helix: 1.11 (0.17), residues: 894 sheet: -0.77 (0.22), residues: 448 loop : -1.07 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 34 TYR 0.019 0.001 TYR G 137 PHE 0.028 0.002 PHE K 455 TRP 0.010 0.001 TRP H 564 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00467 (23250) covalent geometry : angle 0.59099 (31763) hydrogen bonds : bond 0.03739 ( 930) hydrogen bonds : angle 4.92380 ( 2717) metal coordination : bond 0.00906 ( 33) metal coordination : angle 7.88878 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 376 time to evaluate : 0.742 Fit side-chains REVERT: A 191 GLU cc_start: 0.7304 (tt0) cc_final: 0.6867 (mm-30) REVERT: B 9 TYR cc_start: 0.8882 (m-80) cc_final: 0.8451 (m-80) REVERT: B 64 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8078 (tttm) REVERT: B 69 ASN cc_start: 0.7886 (t0) cc_final: 0.7632 (t0) REVERT: C 25 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.7837 (ttt180) REVERT: C 34 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8083 (ttp80) REVERT: C 93 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8152 (mmm) REVERT: C 154 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: C 187 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: D 3 LYS cc_start: 0.8516 (mttm) cc_final: 0.7856 (mtpt) REVERT: D 34 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7730 (ttm110) REVERT: D 111 GLU cc_start: 0.8716 (pp20) cc_final: 0.8491 (pm20) REVERT: D 123 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: E 32 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: E 72 ASP cc_start: 0.8236 (t70) cc_final: 0.7898 (t70) REVERT: E 75 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: E 83 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7695 (mpp-170) REVERT: E 102 ASP cc_start: 0.8483 (m-30) cc_final: 0.8108 (t0) REVERT: E 112 GLN cc_start: 0.8532 (mp10) cc_final: 0.8314 (mt0) REVERT: E 123 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: E 154 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: E 170 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: F 5 MET cc_start: 0.7929 (ttm) cc_final: 0.7623 (ttp) REVERT: F 41 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7932 (mtmt) REVERT: F 92 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7890 (t) REVERT: F 98 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7540 (mtm110) REVERT: F 187 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: G 9 GLU cc_start: 0.7617 (pt0) cc_final: 0.7283 (tt0) REVERT: G 55 ASP cc_start: 0.6067 (m-30) cc_final: 0.5357 (t70) REVERT: G 61 PHE cc_start: 0.7056 (m-80) cc_final: 0.6642 (m-80) REVERT: G 98 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.8096 (mmt90) REVERT: G 103 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.6390 (mmm160) REVERT: G 116 TYR cc_start: 0.8783 (m-80) cc_final: 0.8519 (m-80) REVERT: H 91 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: H 135 GLU cc_start: 0.8174 (tt0) cc_final: 0.7944 (tt0) REVERT: H 178 MET cc_start: 0.7563 (mpt) cc_final: 0.7234 (mtm) REVERT: H 287 ASN cc_start: 0.7537 (t0) cc_final: 0.7263 (t0) REVERT: H 392 LYS cc_start: 0.8281 (ttmt) cc_final: 0.8028 (ttmp) REVERT: H 418 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: H 445 CYS cc_start: 0.7836 (p) cc_final: 0.7612 (m) REVERT: H 461 GLU cc_start: 0.7066 (tt0) cc_final: 0.6813 (mt-10) REVERT: H 568 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: I 476 MET cc_start: 0.6290 (ppp) cc_final: 0.5921 (tpt) REVERT: I 477 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6374 (mp) REVERT: I 577 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: I 594 ASP cc_start: 0.8410 (p0) cc_final: 0.8195 (p0) REVERT: J 33 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8226 (mmtm) REVERT: J 123 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: J 137 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: J 152 ASN cc_start: 0.8403 (t0) cc_final: 0.7858 (t0) REVERT: K 161 ASN cc_start: 0.7672 (t0) cc_final: 0.6888 (p0) REVERT: K 518 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: K 554 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7335 (ttm110) REVERT: K 595 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6328 (tttm) REVERT: L 443 ASN cc_start: 0.5985 (m-40) cc_final: 0.5482 (p0) REVERT: L 476 MET cc_start: 0.7914 (mmm) cc_final: 0.7648 (mmp) REVERT: L 518 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: L 551 GLN cc_start: 0.7815 (tt0) cc_final: 0.7608 (tt0) REVERT: L 575 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: L 581 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: L 600 ASN cc_start: 0.7354 (m-40) cc_final: 0.7040 (m110) outliers start: 132 outliers final: 70 residues processed: 475 average time/residue: 0.6028 time to fit residues: 323.9832 Evaluate side-chains 448 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 351 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 192 ASP 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 154 GLN Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 11 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 123 GLU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 ASP 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 91 GLU Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 554 ARG Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 514 ILE Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 575 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 99 optimal weight: 4.9990 chunk 250 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 195 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 175 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN I 516 ASN I 558 ASN J 45 ASN L 604 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124777 restraints weight = 24899.712| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.01 r_work: 0.3077 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 23283 Z= 0.347 Angle : 0.756 26.656 31799 Z= 0.364 Chirality : 0.047 0.214 3685 Planarity : 0.005 0.055 3736 Dihedral : 14.873 168.951 4236 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.91 % Allowed : 25.22 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2619 helix: 0.89 (0.17), residues: 894 sheet: -0.73 (0.23), residues: 429 loop : -1.06 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 451 TYR 0.020 0.002 TYR G 137 PHE 0.026 0.002 PHE K 455 TRP 0.012 0.002 TRP H 125 HIS 0.006 0.002 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00804 (23250) covalent geometry : angle 0.69282 (31763) hydrogen bonds : bond 0.04236 ( 930) hydrogen bonds : angle 5.11883 ( 2717) metal coordination : bond 0.01255 ( 33) metal coordination : angle 9.01432 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 365 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7267 (tt0) cc_final: 0.6858 (mm-30) REVERT: B 9 TYR cc_start: 0.8939 (m-80) cc_final: 0.8539 (m-80) REVERT: B 64 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8104 (tttm) REVERT: B 93 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (mmt) REVERT: B 116 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7030 (pp20) REVERT: C 25 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.7931 (ttt180) REVERT: C 34 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7919 (ttp80) REVERT: C 93 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8247 (mmt) REVERT: C 154 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: D 3 LYS cc_start: 0.8586 (mttm) cc_final: 0.7827 (mtpt) REVERT: D 34 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7824 (ttm110) REVERT: D 123 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: E 72 ASP cc_start: 0.8261 (t70) cc_final: 0.8030 (t70) REVERT: E 75 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: E 83 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7523 (mpp-170) REVERT: E 123 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: E 154 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: E 170 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: F 5 MET cc_start: 0.7902 (ttm) cc_final: 0.7621 (ttp) REVERT: F 41 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: F 79 ARG cc_start: 0.7544 (mmt180) cc_final: 0.6229 (mmp80) REVERT: F 92 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (t) REVERT: F 187 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: G 9 GLU cc_start: 0.7704 (pt0) cc_final: 0.7403 (tt0) REVERT: G 55 ASP cc_start: 0.5992 (m-30) cc_final: 0.5340 (t70) REVERT: G 61 PHE cc_start: 0.7270 (m-80) cc_final: 0.6884 (m-80) REVERT: G 98 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8154 (mmt90) REVERT: G 103 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.6342 (mmm160) REVERT: G 116 TYR cc_start: 0.8906 (m-80) cc_final: 0.8541 (m-80) REVERT: G 157 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7774 (ttpt) REVERT: H 91 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: H 135 GLU cc_start: 0.8282 (tt0) cc_final: 0.8066 (tt0) REVERT: H 287 ASN cc_start: 0.7565 (t0) cc_final: 0.7288 (t0) REVERT: H 301 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6728 (tm-30) REVERT: H 392 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8170 (ttmm) REVERT: H 418 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: H 432 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: H 461 GLU cc_start: 0.7032 (tt0) cc_final: 0.6773 (mt-10) REVERT: H 536 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7999 (mt-10) REVERT: H 568 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: I 446 ASN cc_start: 0.7047 (p0) cc_final: 0.6454 (p0) REVERT: I 476 MET cc_start: 0.6485 (ppp) cc_final: 0.6047 (tpt) REVERT: I 477 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6426 (mp) REVERT: I 575 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: I 577 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: J 33 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8255 (mmtm) REVERT: J 123 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: J 137 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: J 152 ASN cc_start: 0.8423 (t0) cc_final: 0.7878 (t0) REVERT: J 154 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: K 161 ASN cc_start: 0.7717 (t0) cc_final: 0.6928 (p0) REVERT: K 444 MET cc_start: 0.7740 (mmm) cc_final: 0.6618 (mmm) REVERT: K 484 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8383 (tttp) REVERT: K 518 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: K 595 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6378 (tttm) REVERT: L 443 ASN cc_start: 0.6089 (m-40) cc_final: 0.5499 (p0) REVERT: L 476 MET cc_start: 0.7848 (mmm) cc_final: 0.7609 (mmp) REVERT: L 518 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: L 551 GLN cc_start: 0.7872 (tt0) cc_final: 0.7638 (tt0) REVERT: L 572 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6906 (p) REVERT: L 575 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: L 581 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: L 600 ASN cc_start: 0.7409 (m-40) cc_final: 0.7105 (m110) outliers start: 152 outliers final: 79 residues processed: 473 average time/residue: 0.6021 time to fit residues: 322.7314 Evaluate side-chains 464 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 354 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 39 VAL 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 105 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 11 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 111 GLU 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 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 96 VAL 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 17 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 432 GLU 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 568 GLU Chi-restraints excluded: chain I residue 575 GLU Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 411 ILE Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE 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 572 THR Chi-restraints excluded: chain L residue 575 GLU Chi-restraints excluded: chain L residue 581 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 78 optimal weight: 0.4980 chunk 110 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 C 32 GLN C 112 GLN C 178 ASN D 154 GLN E 112 GLN F 152 ASN F 171 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130020 restraints weight = 24513.962| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.63 r_work: 0.3175 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23283 Z= 0.159 Angle : 0.625 20.725 31799 Z= 0.306 Chirality : 0.042 0.235 3685 Planarity : 0.004 0.037 3736 Dihedral : 14.803 169.888 4234 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.04 % Allowed : 26.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2619 helix: 1.27 (0.17), residues: 894 sheet: -0.73 (0.22), residues: 457 loop : -0.97 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 25 TYR 0.017 0.001 TYR G 141 PHE 0.028 0.002 PHE K 455 TRP 0.011 0.001 TRP H 564 HIS 0.004 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00362 (23250) covalent geometry : angle 0.57563 (31763) hydrogen bonds : bond 0.03663 ( 930) hydrogen bonds : angle 4.79913 ( 2717) metal coordination : bond 0.00752 ( 33) metal coordination : angle 7.24073 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 374 time to evaluate : 0.763 Fit side-chains REVERT: A 191 GLU cc_start: 0.7286 (tt0) cc_final: 0.6855 (mt-10) REVERT: B 9 TYR cc_start: 0.8921 (m-80) cc_final: 0.8420 (m-80) REVERT: B 35 VAL cc_start: 0.8866 (m) cc_final: 0.8619 (p) REVERT: B 93 MET cc_start: 0.8420 (mmm) cc_final: 0.8095 (tpt) REVERT: B 116 GLU cc_start: 0.7349 (pt0) cc_final: 0.7049 (pp20) REVERT: C 25 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.7843 (ttt180) REVERT: C 34 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.8175 (ttp80) REVERT: C 93 MET cc_start: 0.8521 (mmm) cc_final: 0.8206 (mmm) REVERT: C 151 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 154 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7563 (mt0) REVERT: D 3 LYS cc_start: 0.8643 (mttm) cc_final: 0.7957 (mtpt) REVERT: D 34 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7843 (tpt90) REVERT: D 123 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: E 32 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: E 72 ASP cc_start: 0.8197 (t70) cc_final: 0.7945 (t70) REVERT: E 75 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: E 83 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7466 (mpp-170) REVERT: E 102 ASP cc_start: 0.8345 (m-30) cc_final: 0.7943 (t0) REVERT: E 112 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: E 123 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: E 154 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: E 170 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: E 189 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7691 (tppt) REVERT: F 5 MET cc_start: 0.7846 (ttm) cc_final: 0.7557 (ttp) REVERT: F 41 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8045 (mtmt) REVERT: F 79 ARG cc_start: 0.7535 (mmt180) cc_final: 0.6206 (mmp80) REVERT: F 92 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7998 (t) REVERT: F 189 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7694 (mtpm) REVERT: G 9 GLU cc_start: 0.7720 (pt0) cc_final: 0.7442 (tt0) REVERT: G 55 ASP cc_start: 0.5895 (m-30) cc_final: 0.5408 (t70) REVERT: G 61 PHE cc_start: 0.7307 (m-80) cc_final: 0.6969 (m-80) REVERT: G 73 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7991 (pt) REVERT: G 98 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.8215 (mmt90) REVERT: G 103 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6397 (mmm160) REVERT: G 116 TYR cc_start: 0.8890 (m-80) cc_final: 0.8627 (m-80) REVERT: G 157 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7763 (ttpt) REVERT: H 26 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7845 (tt) REVERT: H 54 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8116 (mmtm) REVERT: H 91 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: H 130 ASP cc_start: 0.8119 (p0) cc_final: 0.7675 (p0) REVERT: H 254 ASP cc_start: 0.7994 (t0) cc_final: 0.7167 (p0) REVERT: H 287 ASN cc_start: 0.7530 (t0) cc_final: 0.7307 (t0) REVERT: H 392 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8080 (ttmm) REVERT: H 418 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: H 461 GLU cc_start: 0.7075 (tt0) cc_final: 0.6837 (mt-10) REVERT: H 568 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: I 476 MET cc_start: 0.6649 (ppp) cc_final: 0.6006 (tpt) REVERT: I 477 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6348 (mp) REVERT: I 577 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: J 33 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8245 (mmtm) REVERT: J 62 MET cc_start: 0.8963 (mtp) cc_final: 0.8745 (mtp) REVERT: J 123 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: J 137 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: J 152 ASN cc_start: 0.8340 (t0) cc_final: 0.7983 (t0) REVERT: K 161 ASN cc_start: 0.7649 (t0) cc_final: 0.6883 (p0) REVERT: K 444 MET cc_start: 0.7821 (mmm) cc_final: 0.6719 (mmm) REVERT: K 518 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: K 595 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6409 (tttm) REVERT: L 443 ASN cc_start: 0.6133 (m-40) cc_final: 0.5529 (p0) REVERT: L 476 MET cc_start: 0.7820 (mmm) cc_final: 0.7580 (mtt) REVERT: L 518 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: L 572 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6854 (p) REVERT: L 575 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: L 581 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: L 600 ASN cc_start: 0.7344 (m-40) cc_final: 0.7035 (m110) outliers start: 111 outliers final: 45 residues processed: 455 average time/residue: 0.6223 time to fit residues: 320.0405 Evaluate side-chains 421 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 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 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 411 ILE Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 578 LYS Chi-restraints excluded: chain K residue 595 LYS 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 572 THR Chi-restraints excluded: chain L residue 575 GLU Chi-restraints excluded: chain L residue 581 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 136 optimal weight: 0.0970 chunk 187 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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 C 32 GLN D 154 GLN E 112 GLN F 171 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 344 GLN ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128235 restraints weight = 24411.346| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.65 r_work: 0.3190 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23283 Z= 0.159 Angle : 0.622 20.332 31799 Z= 0.304 Chirality : 0.042 0.233 3685 Planarity : 0.004 0.041 3736 Dihedral : 14.773 171.001 4234 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.54 % Allowed : 27.76 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2619 helix: 1.43 (0.17), residues: 894 sheet: -0.84 (0.22), residues: 483 loop : -0.87 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 25 TYR 0.014 0.001 TYR G 137 PHE 0.028 0.002 PHE K 455 TRP 0.009 0.001 TRP H 564 HIS 0.004 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00363 (23250) covalent geometry : angle 0.57668 (31763) hydrogen bonds : bond 0.03540 ( 930) hydrogen bonds : angle 4.71455 ( 2717) metal coordination : bond 0.00718 ( 33) metal coordination : angle 6.94622 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 366 time to evaluate : 0.690 Fit side-chains REVERT: A 191 GLU cc_start: 0.7443 (tt0) cc_final: 0.6971 (mm-30) REVERT: B 9 TYR cc_start: 0.8897 (m-80) cc_final: 0.8379 (m-80) REVERT: B 35 VAL cc_start: 0.8860 (m) cc_final: 0.8607 (p) REVERT: B 116 GLU cc_start: 0.7330 (pt0) cc_final: 0.7043 (pp20) REVERT: C 25 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7772 (ttt180) REVERT: C 34 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8127 (ttp80) REVERT: C 93 MET cc_start: 0.8522 (mmm) cc_final: 0.8171 (mmm) REVERT: C 151 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8547 (p) REVERT: C 154 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: C 187 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: D 3 LYS cc_start: 0.8620 (mttm) cc_final: 0.7924 (mtpt) REVERT: D 34 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7707 (ttm110) REVERT: D 123 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: E 32 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: E 72 ASP cc_start: 0.8173 (t70) cc_final: 0.7914 (t70) REVERT: E 75 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: E 83 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7512 (mpp-170) REVERT: E 102 ASP cc_start: 0.8318 (m-30) cc_final: 0.7930 (t0) REVERT: E 112 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: E 123 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: E 154 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: E 170 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: E 189 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7691 (tppt) REVERT: F 5 MET cc_start: 0.7866 (ttm) cc_final: 0.7498 (ttp) REVERT: F 41 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7933 (mtmt) REVERT: F 79 ARG cc_start: 0.7531 (mmt180) cc_final: 0.6197 (mmp80) REVERT: F 92 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.8007 (t) REVERT: F 189 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7681 (mtpm) REVERT: G 9 GLU cc_start: 0.7672 (pt0) cc_final: 0.7419 (tt0) REVERT: G 55 ASP cc_start: 0.6110 (m-30) cc_final: 0.5510 (t0) REVERT: G 61 PHE cc_start: 0.7319 (m-80) cc_final: 0.6985 (m-80) REVERT: G 73 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7935 (pt) REVERT: G 98 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.8171 (mmt90) REVERT: G 103 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.6379 (mmm160) REVERT: G 116 TYR cc_start: 0.8892 (m-80) cc_final: 0.8633 (m-80) REVERT: G 157 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7666 (ttpt) REVERT: H 26 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7794 (tt) REVERT: H 54 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8071 (mmtm) REVERT: H 91 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: H 287 ASN cc_start: 0.7476 (t0) cc_final: 0.7258 (t0) REVERT: H 392 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8129 (ttmm) REVERT: H 418 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: H 461 GLU cc_start: 0.7065 (tt0) cc_final: 0.6839 (mt-10) REVERT: H 568 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: I 446 ASN cc_start: 0.6689 (p0) cc_final: 0.6294 (p0) REVERT: I 476 MET cc_start: 0.6730 (ppp) cc_final: 0.5923 (tpt) REVERT: I 477 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6285 (mp) REVERT: I 577 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: J 33 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8211 (mmtm) REVERT: J 62 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8709 (mtp) REVERT: J 137 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: J 152 ASN cc_start: 0.8325 (t0) cc_final: 0.7995 (t0) REVERT: K 161 ASN cc_start: 0.7635 (t0) cc_final: 0.6904 (p0) REVERT: K 444 MET cc_start: 0.7837 (mmm) cc_final: 0.7000 (mmm) REVERT: K 518 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: K 595 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6355 (tttm) REVERT: L 443 ASN cc_start: 0.6074 (m-40) cc_final: 0.5451 (p0) REVERT: L 476 MET cc_start: 0.7914 (mmm) cc_final: 0.7632 (mmp) REVERT: L 518 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: L 572 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6786 (p) REVERT: L 575 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: L 581 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: L 600 ASN cc_start: 0.7341 (m-40) cc_final: 0.7024 (m110) outliers start: 100 outliers final: 47 residues processed: 437 average time/residue: 0.6065 time to fit residues: 300.3510 Evaluate side-chains 426 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 350 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 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 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 92 TYR 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 26 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain 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 62 MET Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 411 ILE Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 575 GLU Chi-restraints excluded: chain L residue 581 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 145 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 60 optimal weight: 0.0170 chunk 248 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- 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 C 32 GLN D 154 GLN E 112 GLN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 175 GLN ** H 344 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.167925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126567 restraints weight = 24602.786| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.69 r_work: 0.3162 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23283 Z= 0.204 Angle : 0.650 21.829 31799 Z= 0.317 Chirality : 0.043 0.215 3685 Planarity : 0.004 0.046 3736 Dihedral : 14.738 170.991 4234 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.45 % Allowed : 27.99 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2619 helix: 1.42 (0.17), residues: 894 sheet: -0.79 (0.22), residues: 488 loop : -0.88 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 210 TYR 0.021 0.001 TYR G 141 PHE 0.031 0.002 PHE H 249 TRP 0.009 0.001 TRP H 564 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00470 (23250) covalent geometry : angle 0.60246 (31763) hydrogen bonds : bond 0.03627 ( 930) hydrogen bonds : angle 4.75480 ( 2717) metal coordination : bond 0.00827 ( 33) metal coordination : angle 7.25958 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 354 time to evaluate : 0.786 Fit side-chains REVERT: A 191 GLU cc_start: 0.7461 (tt0) cc_final: 0.6966 (mm-30) REVERT: B 9 TYR cc_start: 0.8921 (m-80) cc_final: 0.8397 (m-80) REVERT: B 35 VAL cc_start: 0.8850 (m) cc_final: 0.8597 (p) REVERT: B 116 GLU cc_start: 0.7334 (pt0) cc_final: 0.7029 (pp20) REVERT: C 25 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.7805 (ttt180) REVERT: C 34 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.8075 (ttp80) REVERT: C 93 MET cc_start: 0.8534 (mmm) cc_final: 0.8245 (mmm) REVERT: C 151 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8523 (p) REVERT: C 154 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: D 3 LYS cc_start: 0.8633 (mttm) cc_final: 0.7927 (mtpt) REVERT: D 34 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7777 (ttm110) REVERT: D 123 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: E 32 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: E 72 ASP cc_start: 0.8152 (t70) cc_final: 0.7916 (t70) REVERT: E 75 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: E 83 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7522 (mpp-170) REVERT: E 102 ASP cc_start: 0.8354 (m-30) cc_final: 0.7954 (t0) REVERT: E 112 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: E 123 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: E 154 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: E 170 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: F 5 MET cc_start: 0.7883 (ttm) cc_final: 0.7525 (ttp) REVERT: F 41 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: F 79 ARG cc_start: 0.7528 (mmt180) cc_final: 0.6197 (mmp80) REVERT: F 92 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8019 (t) REVERT: F 189 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7708 (mtpm) REVERT: G 9 GLU cc_start: 0.7703 (pt0) cc_final: 0.7454 (tt0) REVERT: G 55 ASP cc_start: 0.6156 (m-30) cc_final: 0.5568 (t0) REVERT: G 61 PHE cc_start: 0.7336 (m-80) cc_final: 0.7019 (m-80) REVERT: G 98 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8156 (mmt90) REVERT: G 103 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.6406 (mmm160) REVERT: G 116 TYR cc_start: 0.8930 (m-80) cc_final: 0.8575 (m-80) REVERT: G 157 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7718 (ttpt) REVERT: H 26 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7826 (tt) REVERT: H 54 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8144 (mmtm) REVERT: H 91 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: H 175 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5460 (mt0) REVERT: H 287 ASN cc_start: 0.7472 (t0) cc_final: 0.7099 (t0) REVERT: H 392 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8159 (ttmm) REVERT: H 418 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: H 568 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: I 446 ASN cc_start: 0.6660 (p0) cc_final: 0.6368 (p0) REVERT: I 476 MET cc_start: 0.6737 (ppp) cc_final: 0.5857 (tpt) REVERT: I 477 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6225 (mp) REVERT: I 577 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: J 33 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8220 (mmtm) REVERT: J 62 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8752 (mtp) REVERT: J 137 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: J 152 ASN cc_start: 0.8347 (t0) cc_final: 0.7912 (t0) REVERT: K 161 ASN cc_start: 0.7635 (t0) cc_final: 0.6905 (p0) REVERT: K 444 MET cc_start: 0.7874 (mmm) cc_final: 0.7047 (mmm) REVERT: K 484 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8409 (tttp) REVERT: K 518 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: K 595 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6388 (tttm) REVERT: L 443 ASN cc_start: 0.6119 (m-40) cc_final: 0.5479 (p0) REVERT: L 476 MET cc_start: 0.7860 (mmm) cc_final: 0.7573 (mmp) REVERT: L 518 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: L 572 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6791 (p) REVERT: L 575 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: L 581 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: L 600 ASN cc_start: 0.7367 (m-40) cc_final: 0.7054 (m110) outliers start: 98 outliers final: 52 residues processed: 426 average time/residue: 0.6167 time to fit residues: 297.0099 Evaluate side-chains 427 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 346 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 145 THR 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 105 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 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 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 150 ILE 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 26 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 175 GLN Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 304 ASN Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 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 62 MET Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 411 ILE Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 575 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 88 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 32 GLN C 112 GLN C 178 ASN D 154 GLN E 112 GLN F 171 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN H 344 GLN ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 ASN J 45 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129237 restraints weight = 24442.794| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.70 r_work: 0.3203 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23283 Z= 0.138 Angle : 0.614 19.523 31799 Z= 0.301 Chirality : 0.041 0.244 3685 Planarity : 0.004 0.039 3736 Dihedral : 14.739 171.954 4234 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.68 % Allowed : 28.90 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.16), residues: 2619 helix: 1.56 (0.18), residues: 894 sheet: -0.73 (0.22), residues: 487 loop : -0.83 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 25 TYR 0.015 0.001 TYR I 599 PHE 0.033 0.002 PHE H 249 TRP 0.009 0.001 TRP H 564 HIS 0.003 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00311 (23250) covalent geometry : angle 0.57326 (31763) hydrogen bonds : bond 0.03501 ( 930) hydrogen bonds : angle 4.64999 ( 2717) metal coordination : bond 0.00655 ( 33) metal coordination : angle 6.59776 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 371 time to evaluate : 0.897 Fit side-chains REVERT: B 9 TYR cc_start: 0.8861 (m-80) cc_final: 0.8285 (m-80) REVERT: B 69 ASN cc_start: 0.7869 (t0) cc_final: 0.7610 (t0) REVERT: B 116 GLU cc_start: 0.7236 (pt0) cc_final: 0.6936 (pp20) REVERT: C 25 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7778 (ttt180) REVERT: C 34 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8166 (ttp80) REVERT: C 93 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: C 154 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: D 3 LYS cc_start: 0.8632 (mttm) cc_final: 0.7933 (mtpt) REVERT: D 123 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: E 32 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: E 72 ASP cc_start: 0.8151 (t70) cc_final: 0.7869 (t70) REVERT: E 75 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: E 83 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7529 (mpp-170) REVERT: E 102 ASP cc_start: 0.8324 (m-30) cc_final: 0.7959 (t0) REVERT: E 112 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: E 154 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: E 170 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: F 41 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7928 (mtmt) REVERT: F 79 ARG cc_start: 0.7504 (mmt180) cc_final: 0.6174 (mmp80) REVERT: F 92 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8009 (t) REVERT: F 189 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7711 (mtpm) REVERT: G 9 GLU cc_start: 0.7693 (pt0) cc_final: 0.7443 (tt0) REVERT: G 55 ASP cc_start: 0.6101 (m-30) cc_final: 0.5495 (t0) REVERT: G 61 PHE cc_start: 0.7325 (m-80) cc_final: 0.6976 (m-80) REVERT: G 98 ARG cc_start: 0.8452 (mmt-90) cc_final: 0.8124 (mmt90) REVERT: G 103 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6385 (mmm160) REVERT: G 116 TYR cc_start: 0.8900 (m-80) cc_final: 0.8629 (m-80) REVERT: G 157 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7732 (ttpt) REVERT: H 26 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7788 (tt) REVERT: H 54 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8080 (mmtm) REVERT: H 91 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: H 130 ASP cc_start: 0.8051 (p0) cc_final: 0.7574 (p0) REVERT: H 175 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5556 (mt0) REVERT: H 287 ASN cc_start: 0.7441 (t0) cc_final: 0.7053 (t0) REVERT: H 340 PHE cc_start: 0.8295 (m-80) cc_final: 0.8086 (m-80) REVERT: H 418 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6698 (tm-30) REVERT: H 568 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: I 476 MET cc_start: 0.6737 (ppp) cc_final: 0.5712 (tpt) REVERT: I 515 GLU cc_start: 0.8542 (tt0) cc_final: 0.8316 (tt0) REVERT: I 577 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7502 (tp30) REVERT: J 33 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8214 (mmtm) REVERT: J 137 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: J 152 ASN cc_start: 0.8276 (t0) cc_final: 0.7953 (t0) REVERT: K 161 ASN cc_start: 0.7610 (t0) cc_final: 0.6897 (p0) REVERT: K 444 MET cc_start: 0.7711 (mmm) cc_final: 0.6956 (mmm) REVERT: K 484 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8396 (tttp) REVERT: K 518 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: K 595 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6355 (tttm) REVERT: L 443 ASN cc_start: 0.6115 (m-40) cc_final: 0.5485 (p0) REVERT: L 476 MET cc_start: 0.7807 (mmm) cc_final: 0.7524 (mmp) REVERT: L 518 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: L 572 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6773 (p) REVERT: L 575 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: L 581 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: L 600 ASN cc_start: 0.7250 (m-40) cc_final: 0.6940 (m110) outliers start: 81 outliers final: 47 residues processed: 424 average time/residue: 0.6521 time to fit residues: 311.8527 Evaluate side-chains 423 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 351 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain A residue 145 THR 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 154 GLN Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain 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 26 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 175 GLN Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 418 GLU Chi-restraints excluded: chain H residue 444 MET Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 568 GLU Chi-restraints excluded: chain I residue 460 VAL Chi-restraints excluded: chain I residue 577 GLU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 411 ILE Chi-restraints excluded: chain K residue 438 ASN Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 518 GLU Chi-restraints excluded: chain K residue 549 ILE Chi-restraints excluded: chain K residue 595 LYS Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 518 GLU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 575 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 237 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 253 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 C 32 GLN D 154 GLN E 112 GLN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN H 479 ASN I 483 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 = 0.3959 r_free = 0.3959 target = 0.167870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127525 restraints weight = 24516.108| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.81 r_work: 0.3174 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23283 Z= 0.184 Angle : 0.638 20.501 31799 Z= 0.312 Chirality : 0.042 0.227 3685 Planarity : 0.004 0.048 3736 Dihedral : 14.696 171.990 4234 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.73 % Allowed : 29.08 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.16), residues: 2619 helix: 1.56 (0.18), residues: 894 sheet: -0.72 (0.22), residues: 488 loop : -0.83 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 25 TYR 0.024 0.001 TYR G 141 PHE 0.032 0.002 PHE H 249 TRP 0.009 0.001 TRP H 564 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00425 (23250) covalent geometry : angle 0.59584 (31763) hydrogen bonds : bond 0.03551 ( 930) hydrogen bonds : angle 4.64478 ( 2717) metal coordination : bond 0.00756 ( 33) metal coordination : angle 6.83949 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.70 seconds wall clock time: 135 minutes 7.86 seconds (8107.86 seconds total)