Starting phenix.real_space_refine on Tue Sep 15 10:00:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.cif" model { file = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z80_11113/09_2026/6z80_11113.cif" } resolution = 3.0 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21340 atoms to isotropic. 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 10 6.06 5 P 30 5.49 5 S 170 5.16 5 C 13520 2.51 5 N 3740 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21460 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "B" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "G" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "I" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "J" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "F" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "N" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "M" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "O" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "P" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "Q" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "R" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} 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: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8GT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' ZN': 1, '8GT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' ZN': 1, '8GT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 579 SG CYS A 141 66.209 29.161 63.192 1.00 0.00 S ATOM 1133 SG CYS A 212 68.433 32.356 65.361 1.00 0.00 S ATOM 2680 SG CYS B 141 85.293 60.978 63.219 1.00 0.00 S ATOM 3234 SG CYS B 212 82.941 64.065 65.410 1.00 0.00 S ATOM 4112 SG CYS C 141 60.877 88.927 63.261 1.00 0.00 S ATOM 4666 SG CYS C 212 57.215 87.640 65.450 1.00 0.00 S ATOM 5544 SG CYS E 141 30.126 37.333 63.246 1.00 0.00 S ATOM 6098 SG CYS E 212 33.850 36.219 65.426 1.00 0.00 S ATOM 6976 SG CYS G 141 26.769 41.963 83.186 1.00 0.00 S ATOM 7530 SG CYS G 212 26.862 45.843 80.996 1.00 0.00 S ATOM 8408 SG CYS H 141 30.052 78.969 83.215 1.00 0.00 S ATOM 8962 SG CYS H 212 33.766 80.090 81.022 1.00 0.00 S ATOM 9840 SG CYS I 141 66.290 87.163 83.194 1.00 0.00 S ATOM 10394 SG CYS I 212 68.508 83.971 81.014 1.00 0.00 S ATOM 11272 SG CYS J 141 85.271 55.282 83.234 1.00 0.00 S ATOM 11826 SG CYS J 212 82.910 52.202 81.042 1.00 0.00 S ATOM 12704 SG CYS F 141 60.807 27.315 83.262 1.00 0.00 S ATOM 13258 SG CYS F 212 57.149 28.614 81.073 1.00 0.00 S ATOM 14136 SG CYS D 141 26.662 74.282 63.285 1.00 0.00 S ATOM 14690 SG CYS D 212 26.776 70.401 65.473 1.00 0.00 S Time building chain proxies: 4.52, per 1000 atoms: 0.21 Number of scatterers: 21460 At special positions: 0 Unit cell: (113.085, 117.393, 147.549, 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 10 29.99 S 170 16.00 P 30 15.00 O 3990 8.00 N 3740 7.00 C 13520 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: 1.48 Conformation dependent library (CDL) restraints added in 929.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 212 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 212 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 212 " pdb="ZN ZN C 302 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 212 " pdb="ZN ZN D 303 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 212 " pdb="ZN ZN E 302 " - pdb=" ND1 HIS E 144 " pdb=" ZN F 303 " pdb="ZN ZN F 303 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 303 " - pdb=" SG CYS F 212 " pdb="ZN ZN F 303 " - pdb=" ND1 HIS F 144 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 212 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 144 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 212 " pdb="ZN ZN H 302 " - pdb=" ND1 HIS H 144 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 212 " pdb="ZN ZN I 302 " - pdb=" ND1 HIS I 144 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 302 " - pdb=" SG CYS J 212 " pdb="ZN ZN J 302 " - pdb=" ND1 HIS J 144 " 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4980 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 0 sheets defined 44.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.869A pdb=" N LEU A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.873A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.739A pdb=" N ARG A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 33 Processing helix chain 'L' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG L 62 " --> pdb=" O ASP L 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG L 63 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.868A pdb=" N LEU B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN B 110 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.739A pdb=" N ARG B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.870A pdb=" N LEU C 92 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.903A pdb=" N SER C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN C 110 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 75 Processing helix chain 'E' and resid 75 through 82 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.868A pdb=" N LEU E 92 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER E 100 " --> pdb=" O TRP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN E 110 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.873A pdb=" N ALA E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.638A pdb=" N LYS E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 248 " --> pdb=" O PHE E 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'G' and resid 75 through 82 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.869A pdb=" N LEU G 92 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER G 100 " --> pdb=" O TRP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN G 110 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 233 through 237 Processing helix chain 'G' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG G 241 " --> pdb=" O ASP G 237 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 75 through 82 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.868A pdb=" N LEU H 92 " --> pdb=" O GLN H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 103 removed outlier: 3.903A pdb=" N SER H 100 " --> pdb=" O TRP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN H 110 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 173 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.638A pdb=" N LYS H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 237 through 248 removed outlier: 3.739A pdb=" N ARG H 241 " --> pdb=" O ASP H 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU H 243 " --> pdb=" O LYS H 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR H 246 " --> pdb=" O GLU H 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE H 248 " --> pdb=" O PHE H 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'I' and resid 75 through 82 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.869A pdb=" N LEU I 92 " --> pdb=" O GLN I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER I 100 " --> pdb=" O TRP I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN I 110 " --> pdb=" O LYS I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 118 removed outlier: 3.990A pdb=" N ASN I 118 " --> pdb=" O SER I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU I 173 " --> pdb=" O ALA I 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 177 " --> pdb=" O GLU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 189 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 215 Processing helix chain 'I' and resid 233 through 237 Processing helix chain 'I' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG I 241 " --> pdb=" O ASP I 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU I 243 " --> pdb=" O LYS I 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE I 244 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR I 246 " --> pdb=" O GLU I 242 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE I 248 " --> pdb=" O PHE I 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 75 Processing helix chain 'J' and resid 75 through 82 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.870A pdb=" N LEU J 92 " --> pdb=" O GLN J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER J 100 " --> pdb=" O TRP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 111 removed outlier: 3.778A pdb=" N GLN J 110 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA J 169 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 215 Processing helix chain 'J' and resid 233 through 237 Processing helix chain 'J' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG J 241 " --> pdb=" O ASP J 237 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU J 243 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 248 " --> pdb=" O PHE J 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 75 through 82 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.869A pdb=" N LEU F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.904A pdb=" N SER F 100 " --> pdb=" O TRP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.779A pdb=" N GLN F 110 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 118 removed outlier: 3.992A pdb=" N ASN F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 3.873A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.637A pdb=" N LYS F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG F 241 " --> pdb=" O ASP F 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 248 " --> pdb=" O PHE F 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.870A pdb=" N LEU D 92 " --> pdb=" O GLN D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.903A pdb=" N SER D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.778A pdb=" N GLN D 110 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 removed outlier: 3.991A pdb=" N ASN D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.874A pdb=" N ALA D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.638A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.740A pdb=" N ARG D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 33 Processing helix chain 'K' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 33 Processing helix chain 'N' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 33 Processing helix chain 'M' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 63 " --> pdb=" O LYS M 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 33 Processing helix chain 'O' and resid 52 through 64 removed outlier: 3.930A pdb=" N ARG O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG O 63 " --> pdb=" O LYS O 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 33 Processing helix chain 'P' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG P 63 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 33 Processing helix chain 'Q' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 33 Processing helix chain 'R' and resid 52 through 64 removed outlier: 3.930A pdb=" N ARG R 62 " --> pdb=" O ASP R 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 33 Processing helix chain 'S' and resid 52 through 64 removed outlier: 3.930A pdb=" N ARG S 62 " --> pdb=" O ASP S 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 33 Processing helix chain 'T' and resid 52 through 64 removed outlier: 3.929A pdb=" N ARG T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG T 63 " --> pdb=" O LYS T 59 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6846 1.34 - 1.45: 3135 1.45 - 1.57: 11509 1.57 - 1.69: 50 1.69 - 1.81: 310 Bond restraints: 21850 Sorted by residual: bond pdb=" O3B 8GT J 301 " pdb=" PG 8GT J 301 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" O3B 8GT H 301 " pdb=" PG 8GT H 301 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" O3B 8GT F 301 " pdb=" PG 8GT F 301 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" O3B 8GT B 301 " pdb=" PG 8GT B 301 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" O3B 8GT D 301 " pdb=" PG 8GT D 301 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 21845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 28601 2.90 - 5.80: 799 5.80 - 8.69: 130 8.69 - 11.59: 20 11.59 - 14.49: 20 Bond angle restraints: 29570 Sorted by residual: angle pdb=" C GLN L 9 " pdb=" N ILE L 10 " pdb=" CA ILE L 10 " ideal model delta sigma weight residual 121.97 130.85 -8.88 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN O 9 " pdb=" N ILE O 10 " pdb=" CA ILE O 10 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN R 9 " pdb=" N ILE R 10 " pdb=" CA ILE R 10 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN N 9 " pdb=" N ILE N 10 " pdb=" CA ILE N 10 " ideal model delta sigma weight residual 121.97 130.83 -8.86 1.80e+00 3.09e-01 2.42e+01 angle pdb=" C GLN S 9 " pdb=" N ILE S 10 " pdb=" CA ILE S 10 " ideal model delta sigma weight residual 121.97 130.83 -8.86 1.80e+00 3.09e-01 2.42e+01 ... (remaining 29565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 12511 14.13 - 28.25: 569 28.25 - 42.38: 318 42.38 - 56.50: 112 56.50 - 70.63: 20 Dihedral angle restraints: 13530 sinusoidal: 5840 harmonic: 7690 Sorted by residual: dihedral pdb=" CA GLN O 9 " pdb=" C GLN O 9 " pdb=" N ILE O 10 " pdb=" CA ILE O 10 " ideal model delta harmonic sigma weight residual -180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLN L 9 " pdb=" C GLN L 9 " pdb=" N ILE L 10 " pdb=" CA ILE L 10 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLN Q 9 " pdb=" C GLN Q 9 " pdb=" N ILE Q 10 " pdb=" CA ILE Q 10 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 13527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2022 0.052 - 0.104: 936 0.104 - 0.155: 322 0.155 - 0.207: 60 0.207 - 0.259: 10 Chirality restraints: 3350 Sorted by residual: chirality pdb=" C2' 8GT D 302 " pdb=" C1' 8GT D 302 " pdb=" C3' 8GT D 302 " pdb=" O2' 8GT D 302 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C2' 8GT F 301 " pdb=" C1' 8GT F 301 " pdb=" C3' 8GT F 301 " pdb=" O2' 8GT F 301 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C2' 8GT J 301 " pdb=" C1' 8GT J 301 " pdb=" C3' 8GT J 301 " pdb=" O2' 8GT J 301 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3347 not shown) Planarity restraints: 3710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 8GT B 301 " -0.059 2.00e-02 2.50e+03 2.84e-02 2.62e+01 pdb=" C2 8GT B 301 " 0.015 2.00e-02 2.50e+03 pdb=" C4 8GT B 301 " -0.014 2.00e-02 2.50e+03 pdb=" C5 8GT B 301 " -0.013 2.00e-02 2.50e+03 pdb=" C6 8GT B 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8 8GT B 301 " 0.018 2.00e-02 2.50e+03 pdb=" N1 8GT B 301 " 0.019 2.00e-02 2.50e+03 pdb=" N2 8GT B 301 " 0.032 2.00e-02 2.50e+03 pdb=" N3 8GT B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N7 8GT B 301 " 0.006 2.00e-02 2.50e+03 pdb=" N9 8GT B 301 " -0.005 2.00e-02 2.50e+03 pdb=" O6 8GT B 301 " -0.042 2.00e-02 2.50e+03 pdb=" O8 8GT B 301 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 8GT D 301 " 0.059 2.00e-02 2.50e+03 2.84e-02 2.62e+01 pdb=" C2 8GT D 301 " -0.015 2.00e-02 2.50e+03 pdb=" C4 8GT D 301 " 0.014 2.00e-02 2.50e+03 pdb=" C5 8GT D 301 " 0.013 2.00e-02 2.50e+03 pdb=" C6 8GT D 301 " 0.007 2.00e-02 2.50e+03 pdb=" C8 8GT D 301 " -0.018 2.00e-02 2.50e+03 pdb=" N1 8GT D 301 " -0.018 2.00e-02 2.50e+03 pdb=" N2 8GT D 301 " -0.032 2.00e-02 2.50e+03 pdb=" N3 8GT D 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 8GT D 301 " -0.006 2.00e-02 2.50e+03 pdb=" N9 8GT D 301 " 0.005 2.00e-02 2.50e+03 pdb=" O6 8GT D 301 " 0.042 2.00e-02 2.50e+03 pdb=" O8 8GT D 301 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 8GT F 301 " 0.059 2.00e-02 2.50e+03 2.83e-02 2.61e+01 pdb=" C2 8GT F 301 " -0.015 2.00e-02 2.50e+03 pdb=" C4 8GT F 301 " 0.014 2.00e-02 2.50e+03 pdb=" C5 8GT F 301 " 0.013 2.00e-02 2.50e+03 pdb=" C6 8GT F 301 " 0.006 2.00e-02 2.50e+03 pdb=" C8 8GT F 301 " -0.018 2.00e-02 2.50e+03 pdb=" N1 8GT F 301 " -0.018 2.00e-02 2.50e+03 pdb=" N2 8GT F 301 " -0.032 2.00e-02 2.50e+03 pdb=" N3 8GT F 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 8GT F 301 " -0.006 2.00e-02 2.50e+03 pdb=" N9 8GT F 301 " 0.005 2.00e-02 2.50e+03 pdb=" O6 8GT F 301 " 0.042 2.00e-02 2.50e+03 pdb=" O8 8GT F 301 " -0.053 2.00e-02 2.50e+03 ... (remaining 3707 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 185 2.60 - 3.18: 16017 3.18 - 3.75: 31007 3.75 - 4.33: 46753 4.33 - 4.90: 80260 Nonbonded interactions: 174222 Sorted by model distance: nonbonded pdb=" O8 8GT E 301 " pdb="ZN ZN E 302 " model vdw 2.030 2.230 nonbonded pdb="ZN ZN H 302 " pdb=" O8 8GT I 301 " model vdw 2.131 2.230 nonbonded pdb=" O8 8GT F 301 " pdb="ZN ZN F 303 " model vdw 2.144 2.230 nonbonded pdb=" O8 8GT D 301 " pdb="ZN ZN D 303 " model vdw 2.151 2.230 nonbonded pdb="ZN ZN A 301 " pdb=" O8 8GT B 301 " model vdw 2.172 2.230 ... (remaining 174217 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'K' selection = chain 'N' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'D' } 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.890 Find NCS groups from input model: 0.170 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.016 0.501 21880 Z= 0.582 Angle : 1.242 14.491 29570 Z= 0.661 Chirality : 0.065 0.259 3350 Planarity : 0.007 0.047 3710 Dihedral : 11.939 70.627 8550 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.45 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.14), residues: 2610 helix: -4.48 (0.08), residues: 890 sheet: 0.34 (0.21), residues: 670 loop : -2.27 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.031 0.004 TYR I 75 PHE 0.035 0.005 PHE A 234 TRP 0.011 0.002 TRP E 96 HIS 0.010 0.002 HIS J 210 Details of bonding type rmsd/Z covalent geometry : bond 0.01013 / 0.43 (21850) covalent geometry : angle 1.24166 / 0.66 (29570) hydrogen bonds : bond 0.36043 / 23.32 ( 501) hydrogen bonds : angle 10.81687 / 7.41 ( 1443) metal coordination : bond 0.31911 / 21.00 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 1.121 Fit side-chains REVERT: A 93 LYS cc_start: 0.7665 (mttm) cc_final: 0.6762 (tttm) REVERT: A 175 TYR cc_start: 0.8427 (m-80) cc_final: 0.8151 (m-80) REVERT: A 238 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7987 (Cg_exo) REVERT: B 93 LYS cc_start: 0.7470 (mttm) cc_final: 0.6406 (tttm) REVERT: B 175 TYR cc_start: 0.8467 (m-80) cc_final: 0.8236 (m-80) REVERT: B 213 MET cc_start: 0.7943 (mtp) cc_final: 0.7689 (mtm) REVERT: C 175 TYR cc_start: 0.8273 (m-80) cc_final: 0.7981 (m-80) REVERT: C 241 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7497 (ttm170) REVERT: C 246 THR cc_start: 0.8581 (m) cc_final: 0.8218 (p) REVERT: E 175 TYR cc_start: 0.8405 (m-80) cc_final: 0.8175 (m-80) REVERT: E 213 MET cc_start: 0.7877 (mtp) cc_final: 0.7547 (mtm) REVERT: E 241 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7424 (ttm110) REVERT: G 93 LYS cc_start: 0.7574 (mttm) cc_final: 0.6841 (tttm) REVERT: G 175 TYR cc_start: 0.8384 (m-80) cc_final: 0.8056 (m-80) REVERT: H 173 GLU cc_start: 0.5590 (tp30) cc_final: 0.5326 (tp30) REVERT: H 213 MET cc_start: 0.7857 (mtp) cc_final: 0.7468 (mtm) REVERT: I 93 LYS cc_start: 0.7578 (mttm) cc_final: 0.6730 (tttm) REVERT: I 140 MET cc_start: 0.7124 (mmm) cc_final: 0.6765 (mmm) REVERT: I 175 TYR cc_start: 0.8443 (m-80) cc_final: 0.8192 (m-80) REVERT: J 93 LYS cc_start: 0.7505 (mttm) cc_final: 0.6627 (tttm) REVERT: J 175 TYR cc_start: 0.8434 (m-80) cc_final: 0.8193 (m-80) REVERT: J 213 MET cc_start: 0.8017 (mtp) cc_final: 0.7741 (mtm) REVERT: F 175 TYR cc_start: 0.8108 (m-80) cc_final: 0.7781 (m-80) REVERT: F 213 MET cc_start: 0.7963 (mtp) cc_final: 0.7718 (mtp) REVERT: F 246 THR cc_start: 0.8339 (m) cc_final: 0.7844 (p) REVERT: D 175 TYR cc_start: 0.8191 (m-80) cc_final: 0.7783 (m-80) REVERT: N 12 MET cc_start: 0.6400 (ptt) cc_final: 0.6017 (ptt) REVERT: T 13 GLU cc_start: 0.7018 (mp0) cc_final: 0.6694 (mp0) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 0.7537 time to fit residues: 534.9093 Evaluate side-chains 496 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 188 GLN L 31 HIS B 126 HIS B 188 GLN C 126 HIS E 126 HIS G 126 HIS G 188 GLN H 126 HIS I 126 HIS J 126 HIS J 180 GLN J 188 GLN F 126 HIS D 126 HIS D 188 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS O 31 HIS O 82 HIS P 31 HIS Q 31 HIS Q 82 HIS ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 ASN S 31 HIS T 31 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.214183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.193832 restraints weight = 21989.348| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.37 r_work: 0.4134 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21880 Z= 0.120 Angle : 0.623 6.541 29570 Z= 0.325 Chirality : 0.047 0.151 3350 Planarity : 0.005 0.038 3710 Dihedral : 9.232 42.228 3270 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.63 % Allowed : 9.57 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.14), residues: 2610 helix: -2.90 (0.12), residues: 1010 sheet: 0.18 (0.21), residues: 640 loop : -1.80 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 62 TYR 0.008 0.001 TYR H 75 PHE 0.013 0.002 PHE F 148 TRP 0.007 0.001 TRP N 79 HIS 0.012 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21850) covalent geometry : angle 0.62259 / 0.32 (29570) hydrogen bonds : bond 0.05537 / 3.61 ( 501) hydrogen bonds : angle 5.76389 / 4.00 ( 1443) metal coordination : bond 0.01073 / 0.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 488 time to evaluate : 0.865 Fit side-chains REVERT: A 93 LYS cc_start: 0.7134 (mttm) cc_final: 0.5494 (tttm) REVERT: A 173 GLU cc_start: 0.6067 (tp30) cc_final: 0.5608 (tp30) REVERT: L 22 GLU cc_start: 0.6999 (pm20) cc_final: 0.6792 (pm20) REVERT: B 93 LYS cc_start: 0.7123 (mttm) cc_final: 0.5476 (tttm) REVERT: B 213 MET cc_start: 0.8061 (mtp) cc_final: 0.7779 (mtm) REVERT: C 70 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6451 (t0) REVERT: C 219 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6847 (mt0) REVERT: E 112 THR cc_start: 0.6152 (m) cc_final: 0.5837 (t) REVERT: E 213 MET cc_start: 0.7945 (mtp) cc_final: 0.7452 (mtm) REVERT: E 219 GLN cc_start: 0.7314 (mt0) cc_final: 0.6674 (mt0) REVERT: G 93 LYS cc_start: 0.7118 (mttm) cc_final: 0.5449 (tttm) REVERT: G 219 GLN cc_start: 0.7055 (mt0) cc_final: 0.6534 (mt0) REVERT: H 133 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8223 (pttp) REVERT: H 173 GLU cc_start: 0.6105 (tp30) cc_final: 0.5624 (tp30) REVERT: H 213 MET cc_start: 0.7939 (mtp) cc_final: 0.7442 (mtm) REVERT: H 223 SER cc_start: 0.8756 (m) cc_final: 0.8539 (m) REVERT: H 239 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7489 (mmmt) REVERT: I 93 LYS cc_start: 0.7211 (mttm) cc_final: 0.5649 (tttm) REVERT: J 93 LYS cc_start: 0.7132 (mttm) cc_final: 0.5709 (tttm) REVERT: J 174 ILE cc_start: 0.7550 (mt) cc_final: 0.7155 (mp) REVERT: J 213 MET cc_start: 0.8153 (mtp) cc_final: 0.7865 (mtm) REVERT: J 219 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7031 (mt0) REVERT: J 242 GLU cc_start: 0.7930 (tp30) cc_final: 0.7705 (tp30) REVERT: F 219 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: F 239 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7182 (mmmt) REVERT: D 102 MET cc_start: 0.5935 (tpt) cc_final: 0.4633 (tpt) REVERT: D 118 ASN cc_start: 0.7108 (t0) cc_final: 0.6611 (t0) REVERT: D 219 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: D 242 GLU cc_start: 0.7855 (tp30) cc_final: 0.7446 (tp30) REVERT: N 12 MET cc_start: 0.6885 (ptt) cc_final: 0.6359 (ptt) REVERT: M 3 TYR cc_start: 0.6934 (m-80) cc_final: 0.6684 (m-80) REVERT: O 22 GLU cc_start: 0.7011 (pm20) cc_final: 0.6749 (pm20) REVERT: O 62 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7682 (mtm110) REVERT: P 50 ASP cc_start: 0.7260 (t70) cc_final: 0.7039 (t70) outliers start: 85 outliers final: 27 residues processed: 522 average time/residue: 0.6988 time to fit residues: 411.7630 Evaluate side-chains 459 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 424 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 168 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 185 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN L 42 ASN B 188 GLN G 143 HIS G 188 GLN I 188 GLN J 188 GLN F 188 GLN D 143 HIS D 188 GLN K 31 HIS N 42 ASN N 82 HIS O 42 ASN O 82 HIS Q 82 HIS R 31 HIS S 42 ASN T 42 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.214414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194166 restraints weight = 21850.916| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.36 r_work: 0.4138 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21880 Z= 0.104 Angle : 0.552 6.125 29570 Z= 0.288 Chirality : 0.046 0.155 3350 Planarity : 0.004 0.041 3710 Dihedral : 8.610 47.224 3270 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.06 % Allowed : 12.65 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.15), residues: 2610 helix: -1.54 (0.15), residues: 1020 sheet: 0.01 (0.20), residues: 700 loop : -1.42 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 66 TYR 0.009 0.001 TYR H 175 PHE 0.015 0.002 PHE L 44 TRP 0.017 0.001 TRP T 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (21850) covalent geometry : angle 0.55228 / 0.29 (29570) hydrogen bonds : bond 0.04224 / 2.74 ( 501) hydrogen bonds : angle 5.12019 / 3.58 ( 1443) metal coordination : bond 0.00821 / 0.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 435 time to evaluate : 0.858 Fit side-chains REVERT: A 93 LYS cc_start: 0.7115 (mttm) cc_final: 0.5529 (tttm) REVERT: A 173 GLU cc_start: 0.6019 (tp30) cc_final: 0.5506 (tp30) REVERT: A 242 GLU cc_start: 0.7428 (tp30) cc_final: 0.7040 (tp30) REVERT: L 22 GLU cc_start: 0.7081 (pm20) cc_final: 0.6847 (pm20) REVERT: B 93 LYS cc_start: 0.7125 (mttm) cc_final: 0.5478 (tttm) REVERT: B 213 MET cc_start: 0.8155 (mtp) cc_final: 0.7903 (mtm) REVERT: B 219 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: C 102 MET cc_start: 0.5978 (tpt) cc_final: 0.4953 (tpt) REVERT: C 219 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6707 (mt0) REVERT: E 112 THR cc_start: 0.6306 (m) cc_final: 0.6017 (t) REVERT: E 174 ILE cc_start: 0.7468 (mt) cc_final: 0.7110 (mp) REVERT: E 213 MET cc_start: 0.7906 (mtp) cc_final: 0.7421 (mtm) REVERT: G 93 LYS cc_start: 0.7117 (mttm) cc_final: 0.5433 (tttm) REVERT: G 173 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5499 (mm-30) REVERT: G 219 GLN cc_start: 0.6956 (mt0) cc_final: 0.6503 (mt0) REVERT: G 242 GLU cc_start: 0.7876 (tp30) cc_final: 0.7421 (tp30) REVERT: H 133 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8169 (pttp) REVERT: H 173 GLU cc_start: 0.6303 (tp30) cc_final: 0.5724 (tp30) REVERT: H 174 ILE cc_start: 0.7507 (mt) cc_final: 0.7165 (mp) REVERT: H 213 MET cc_start: 0.8040 (mtp) cc_final: 0.7589 (mtm) REVERT: H 223 SER cc_start: 0.8740 (m) cc_final: 0.8526 (m) REVERT: H 242 GLU cc_start: 0.7662 (tp30) cc_final: 0.7177 (tp30) REVERT: I 93 LYS cc_start: 0.7169 (mttm) cc_final: 0.5607 (tttm) REVERT: I 219 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6851 (mt0) REVERT: I 242 GLU cc_start: 0.7574 (tp30) cc_final: 0.7039 (tp30) REVERT: J 93 LYS cc_start: 0.7115 (mttm) cc_final: 0.5646 (tttm) REVERT: J 174 ILE cc_start: 0.7469 (mt) cc_final: 0.7050 (mp) REVERT: J 213 MET cc_start: 0.8194 (mtp) cc_final: 0.7945 (mtm) REVERT: J 219 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: F 102 MET cc_start: 0.6103 (tpt) cc_final: 0.5148 (tpt) REVERT: F 219 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6750 (mt0) REVERT: F 239 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7108 (mmmt) REVERT: D 102 MET cc_start: 0.5543 (tpt) cc_final: 0.4752 (tpt) REVERT: D 118 ASN cc_start: 0.7133 (t0) cc_final: 0.6737 (t0) REVERT: D 219 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6396 (mt0) REVERT: N 12 MET cc_start: 0.6953 (ptt) cc_final: 0.6459 (ptt) REVERT: M 3 TYR cc_start: 0.6790 (m-80) cc_final: 0.6542 (m-80) REVERT: O 22 GLU cc_start: 0.6936 (pm20) cc_final: 0.6647 (pm20) REVERT: P 3 TYR cc_start: 0.6835 (m-80) cc_final: 0.6549 (m-80) REVERT: P 50 ASP cc_start: 0.7304 (t70) cc_final: 0.7016 (t70) REVERT: S 3 TYR cc_start: 0.7366 (m-80) cc_final: 0.7158 (m-80) REVERT: T 22 GLU cc_start: 0.6989 (pm20) cc_final: 0.6758 (pm20) REVERT: T 50 ASP cc_start: 0.7545 (m-30) cc_final: 0.7225 (t70) outliers start: 95 outliers final: 44 residues processed: 475 average time/residue: 0.6887 time to fit residues: 370.1229 Evaluate side-chains 457 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 139 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN B 188 GLN C 188 GLN E 188 GLN E 222 ASN G 143 HIS G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 118 ASN F 188 GLN D 143 HIS D 188 GLN O 31 HIS Q 82 HIS R 31 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.211067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.190460 restraints weight = 21888.647| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.36 r_work: 0.4102 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21880 Z= 0.146 Angle : 0.598 8.989 29570 Z= 0.308 Chirality : 0.048 0.156 3350 Planarity : 0.004 0.040 3710 Dihedral : 8.904 50.349 3270 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.44 % Allowed : 13.03 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2610 helix: -1.02 (0.16), residues: 1020 sheet: 0.00 (0.20), residues: 700 loop : -1.36 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 66 TYR 0.015 0.002 TYR H 175 PHE 0.015 0.002 PHE E 148 TRP 0.009 0.001 TRP P 79 HIS 0.005 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (21850) covalent geometry : angle 0.59821 / 0.31 (29570) hydrogen bonds : bond 0.04356 / 2.83 ( 501) hydrogen bonds : angle 5.10662 / 3.58 ( 1443) metal coordination : bond 0.00806 / 0.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 420 time to evaluate : 0.878 Fit side-chains REVERT: A 93 LYS cc_start: 0.7222 (mttm) cc_final: 0.5518 (tttm) REVERT: A 173 GLU cc_start: 0.6230 (tp30) cc_final: 0.5648 (tp30) REVERT: A 242 GLU cc_start: 0.7616 (tp30) cc_final: 0.7259 (tp30) REVERT: B 93 LYS cc_start: 0.7229 (mttm) cc_final: 0.5517 (tttm) REVERT: B 213 MET cc_start: 0.8197 (mtp) cc_final: 0.7976 (mtm) REVERT: C 173 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5602 (mm-30) REVERT: C 215 MET cc_start: 0.8082 (mtp) cc_final: 0.7734 (mtm) REVERT: C 216 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6347 (ptm160) REVERT: C 219 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6770 (mt0) REVERT: C 239 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7010 (mmmt) REVERT: E 213 MET cc_start: 0.7971 (mtp) cc_final: 0.7516 (mtm) REVERT: G 93 LYS cc_start: 0.7224 (mttm) cc_final: 0.5474 (tttm) REVERT: G 173 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5609 (mm-30) REVERT: H 213 MET cc_start: 0.8054 (mtp) cc_final: 0.7554 (mtm) REVERT: I 93 LYS cc_start: 0.7319 (mttm) cc_final: 0.5709 (tttm) REVERT: I 219 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: J 93 LYS cc_start: 0.7147 (mttm) cc_final: 0.5673 (tttm) REVERT: J 174 ILE cc_start: 0.7497 (mt) cc_final: 0.7058 (mp) REVERT: J 213 MET cc_start: 0.8213 (mtp) cc_final: 0.7985 (mtm) REVERT: J 219 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7050 (mt0) REVERT: F 102 MET cc_start: 0.5985 (tpt) cc_final: 0.5185 (tpt) REVERT: F 219 GLN cc_start: 0.7255 (mt0) cc_final: 0.6837 (mt0) REVERT: F 239 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7141 (mmmt) REVERT: D 102 MET cc_start: 0.5569 (tpt) cc_final: 0.4738 (tpt) REVERT: D 173 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5307 (mm-30) REVERT: D 216 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7571 (ptm160) REVERT: D 219 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6452 (mt0) REVERT: M 23 GLN cc_start: 0.6930 (mt0) cc_final: 0.6709 (mt0) REVERT: M 50 ASP cc_start: 0.7643 (m-30) cc_final: 0.7316 (t70) REVERT: O 22 GLU cc_start: 0.7012 (pm20) cc_final: 0.6757 (pm20) REVERT: P 50 ASP cc_start: 0.7356 (t70) cc_final: 0.7068 (t70) REVERT: T 50 ASP cc_start: 0.7563 (m-30) cc_final: 0.7272 (t70) outliers start: 104 outliers final: 51 residues processed: 468 average time/residue: 0.6980 time to fit residues: 368.9066 Evaluate side-chains 464 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 402 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 188 GLN C 188 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN H 188 GLN I 118 ASN I 188 GLN J 188 GLN F 118 ASN F 188 GLN D 188 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.191892 restraints weight = 21738.456| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.36 r_work: 0.4119 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21880 Z= 0.117 Angle : 0.557 7.400 29570 Z= 0.288 Chirality : 0.047 0.150 3350 Planarity : 0.004 0.044 3710 Dihedral : 8.797 55.132 3270 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.87 % Allowed : 13.93 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2610 helix: -0.64 (0.16), residues: 1020 sheet: 0.09 (0.20), residues: 700 loop : -1.21 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 66 TYR 0.016 0.001 TYR G 75 PHE 0.014 0.002 PHE H 148 TRP 0.012 0.001 TRP L 79 HIS 0.008 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21850) covalent geometry : angle 0.55650 / 0.29 (29570) hydrogen bonds : bond 0.03879 / 2.52 ( 501) hydrogen bonds : angle 4.93824 / 3.47 ( 1443) metal coordination : bond 0.00787 / 0.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 417 time to evaluate : 0.848 Fit side-chains REVERT: A 93 LYS cc_start: 0.7157 (mttm) cc_final: 0.5475 (tttm) REVERT: A 173 GLU cc_start: 0.6205 (tp30) cc_final: 0.5626 (tp30) REVERT: B 93 LYS cc_start: 0.7192 (mttm) cc_final: 0.5590 (tttm) REVERT: B 213 MET cc_start: 0.8196 (mtp) cc_final: 0.7965 (mtm) REVERT: B 216 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6725 (ptm160) REVERT: B 219 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: C 70 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6429 (t0) REVERT: C 102 MET cc_start: 0.5925 (tpt) cc_final: 0.5041 (tpt) REVERT: C 173 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5471 (mm-30) REVERT: C 174 ILE cc_start: 0.7719 (mt) cc_final: 0.7358 (mp) REVERT: C 216 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6513 (ptm160) REVERT: C 219 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6718 (mt0) REVERT: E 174 ILE cc_start: 0.7509 (mt) cc_final: 0.7116 (mp) REVERT: E 213 MET cc_start: 0.8017 (mtp) cc_final: 0.7663 (mtm) REVERT: E 216 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7219 (ptm160) REVERT: E 219 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6813 (mt0) REVERT: G 93 LYS cc_start: 0.7193 (mttm) cc_final: 0.5502 (tttm) REVERT: G 102 MET cc_start: 0.5457 (tpt) cc_final: 0.4920 (tpt) REVERT: G 173 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5615 (mm-30) REVERT: G 216 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: H 173 GLU cc_start: 0.6378 (tp30) cc_final: 0.5794 (tp30) REVERT: H 213 MET cc_start: 0.8086 (mtp) cc_final: 0.7681 (mtm) REVERT: I 93 LYS cc_start: 0.7283 (mttm) cc_final: 0.5595 (tttm) REVERT: I 195 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7001 (pt0) REVERT: I 219 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6827 (mt0) REVERT: J 93 LYS cc_start: 0.7143 (mttm) cc_final: 0.5628 (tttm) REVERT: J 174 ILE cc_start: 0.7435 (mt) cc_final: 0.7012 (mp) REVERT: J 213 MET cc_start: 0.8210 (mtp) cc_final: 0.7983 (mtm) REVERT: J 219 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: F 102 MET cc_start: 0.6062 (tpt) cc_final: 0.5203 (tpt) REVERT: F 215 MET cc_start: 0.7994 (mtp) cc_final: 0.7580 (mtm) REVERT: F 219 GLN cc_start: 0.7274 (mt0) cc_final: 0.6856 (mt0) REVERT: F 239 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7109 (mmmt) REVERT: D 102 MET cc_start: 0.5611 (tpt) cc_final: 0.4856 (tpt) REVERT: D 173 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5344 (mm-30) REVERT: D 216 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7469 (ptm160) REVERT: D 219 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6448 (mt0) REVERT: N 12 MET cc_start: 0.6848 (ptt) cc_final: 0.6168 (ptt) REVERT: M 23 GLN cc_start: 0.6887 (mt0) cc_final: 0.6542 (mt0) REVERT: M 50 ASP cc_start: 0.7604 (m-30) cc_final: 0.7288 (t70) REVERT: P 50 ASP cc_start: 0.7324 (t70) cc_final: 0.7060 (t70) REVERT: S 3 TYR cc_start: 0.7370 (m-80) cc_final: 0.7169 (m-80) REVERT: T 36 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7116 (tmtp) REVERT: T 50 ASP cc_start: 0.7537 (m-30) cc_final: 0.7330 (t70) outliers start: 114 outliers final: 55 residues processed: 468 average time/residue: 0.6697 time to fit residues: 355.5131 Evaluate side-chains 468 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 396 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 36 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 236 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 129 optimal weight: 0.0040 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 118 ASN C 188 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 188 GLN J 188 GLN F 118 ASN F 188 GLN D 180 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.212918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192529 restraints weight = 21579.719| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.35 r_work: 0.4126 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21880 Z= 0.114 Angle : 0.554 8.348 29570 Z= 0.285 Chirality : 0.046 0.152 3350 Planarity : 0.004 0.041 3710 Dihedral : 8.789 57.217 3270 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.83 % Allowed : 14.15 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2610 helix: -0.34 (0.17), residues: 1020 sheet: 0.15 (0.20), residues: 700 loop : -1.12 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 66 TYR 0.015 0.001 TYR G 75 PHE 0.014 0.001 PHE E 148 TRP 0.010 0.001 TRP L 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (21850) covalent geometry : angle 0.55386 / 0.28 (29570) hydrogen bonds : bond 0.03687 / 2.39 ( 501) hydrogen bonds : angle 4.86244 / 3.42 ( 1443) metal coordination : bond 0.00682 / 0.43 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 411 time to evaluate : 0.849 Fit side-chains REVERT: A 93 LYS cc_start: 0.7201 (mttm) cc_final: 0.5486 (tttm) REVERT: A 173 GLU cc_start: 0.6233 (tp30) cc_final: 0.5654 (tp30) REVERT: B 93 LYS cc_start: 0.7225 (mttm) cc_final: 0.5630 (tttm) REVERT: B 213 MET cc_start: 0.8195 (mtp) cc_final: 0.7985 (mtm) REVERT: B 216 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6706 (ptm160) REVERT: C 70 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6449 (t0) REVERT: C 102 MET cc_start: 0.5869 (tpt) cc_final: 0.4991 (tpt) REVERT: C 173 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5281 (mm-30) REVERT: C 174 ILE cc_start: 0.7724 (mt) cc_final: 0.7376 (mp) REVERT: C 215 MET cc_start: 0.8031 (mtp) cc_final: 0.7606 (mtm) REVERT: C 216 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6721 (ptm160) REVERT: C 219 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: E 70 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6547 (t0) REVERT: E 102 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5101 (tpt) REVERT: E 140 MET cc_start: 0.8326 (tpt) cc_final: 0.7743 (tpt) REVERT: E 174 ILE cc_start: 0.7502 (mt) cc_final: 0.7117 (mp) REVERT: E 213 MET cc_start: 0.8091 (mtp) cc_final: 0.7722 (mtm) REVERT: E 216 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7249 (ptm160) REVERT: E 219 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6873 (mt0) REVERT: G 70 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6657 (t0) REVERT: G 93 LYS cc_start: 0.7246 (mttm) cc_final: 0.5546 (tttm) REVERT: G 102 MET cc_start: 0.5477 (tpt) cc_final: 0.4916 (tpt) REVERT: G 173 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5508 (mm-30) REVERT: G 216 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: H 102 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4638 (tpt) REVERT: H 173 GLU cc_start: 0.6384 (tp30) cc_final: 0.5771 (tp30) REVERT: H 213 MET cc_start: 0.8154 (mtp) cc_final: 0.7818 (mtm) REVERT: I 93 LYS cc_start: 0.7297 (mttm) cc_final: 0.5605 (tttm) REVERT: I 195 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7020 (pt0) REVERT: I 219 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6836 (mt0) REVERT: J 93 LYS cc_start: 0.7201 (mttm) cc_final: 0.5685 (tttm) REVERT: J 174 ILE cc_start: 0.7451 (mt) cc_final: 0.7051 (mp) REVERT: J 213 MET cc_start: 0.8217 (mtp) cc_final: 0.8006 (mtm) REVERT: J 216 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6837 (ptm160) REVERT: J 219 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: J 223 SER cc_start: 0.8782 (m) cc_final: 0.8572 (m) REVERT: F 102 MET cc_start: 0.5961 (tpt) cc_final: 0.5145 (tpt) REVERT: F 216 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6357 (ptm160) REVERT: F 219 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6849 (mt0) REVERT: D 102 MET cc_start: 0.5463 (tpt) cc_final: 0.4871 (tpt) REVERT: D 173 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5358 (mm-30) REVERT: D 174 ILE cc_start: 0.7461 (mt) cc_final: 0.7137 (mp) REVERT: D 216 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7452 (ptm160) REVERT: D 219 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6461 (mt0) REVERT: N 12 MET cc_start: 0.6821 (ptt) cc_final: 0.6109 (ptt) REVERT: N 50 ASP cc_start: 0.7455 (m-30) cc_final: 0.7139 (t70) REVERT: M 23 GLN cc_start: 0.6964 (mt0) cc_final: 0.6660 (mt0) REVERT: M 50 ASP cc_start: 0.7575 (m-30) cc_final: 0.7287 (t70) REVERT: O 13 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: P 50 ASP cc_start: 0.7440 (t70) cc_final: 0.7163 (t70) REVERT: S 3 TYR cc_start: 0.7402 (m-80) cc_final: 0.7194 (m-80) REVERT: T 36 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7230 (tmtp) outliers start: 113 outliers final: 57 residues processed: 462 average time/residue: 0.6531 time to fit residues: 341.5576 Evaluate side-chains 482 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 402 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 36 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 204 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 180 GLN A 188 GLN B 188 GLN C 118 ASN C 188 GLN E 188 GLN G 188 GLN H 118 ASN H 188 GLN I 118 ASN I 180 GLN I 188 GLN J 188 GLN F 118 ASN F 188 GLN D 118 ASN D 188 GLN K 31 HIS N 31 HIS M 75 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.214401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.193856 restraints weight = 21569.912| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.38 r_work: 0.4136 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21880 Z= 0.100 Angle : 0.534 8.507 29570 Z= 0.275 Chirality : 0.046 0.149 3350 Planarity : 0.004 0.042 3710 Dihedral : 8.632 58.851 3270 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.09 % Allowed : 14.32 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2610 helix: 0.05 (0.17), residues: 1010 sheet: 0.47 (0.21), residues: 640 loop : -1.08 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 66 TYR 0.016 0.001 TYR E 75 PHE 0.013 0.001 PHE J 148 TRP 0.009 0.001 TRP T 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (21850) covalent geometry : angle 0.53392 / 0.27 (29570) hydrogen bonds : bond 0.03401 / 2.21 ( 501) hydrogen bonds : angle 4.75558 / 3.34 ( 1443) metal coordination : bond 0.00650 / 0.41 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 419 time to evaluate : 0.805 Fit side-chains REVERT: A 93 LYS cc_start: 0.7085 (mttm) cc_final: 0.5353 (tttm) REVERT: A 102 MET cc_start: 0.5340 (tpt) cc_final: 0.5121 (tpt) REVERT: A 173 GLU cc_start: 0.6196 (tp30) cc_final: 0.5590 (tp30) REVERT: B 93 LYS cc_start: 0.7147 (mttm) cc_final: 0.5556 (tttm) REVERT: B 213 MET cc_start: 0.8140 (mtp) cc_final: 0.7925 (mtm) REVERT: B 219 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: C 102 MET cc_start: 0.5806 (tpt) cc_final: 0.4939 (tpt) REVERT: C 173 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5406 (mm-30) REVERT: C 174 ILE cc_start: 0.7674 (mt) cc_final: 0.7317 (mp) REVERT: C 215 MET cc_start: 0.7992 (mtp) cc_final: 0.7626 (mtm) REVERT: C 219 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6737 (mt0) REVERT: E 70 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6507 (t0) REVERT: E 93 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7047 (mttt) REVERT: E 102 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.5077 (tpt) REVERT: E 140 MET cc_start: 0.8392 (tpt) cc_final: 0.7712 (tpt) REVERT: E 174 ILE cc_start: 0.7447 (mt) cc_final: 0.7077 (mp) REVERT: E 213 MET cc_start: 0.8021 (mtp) cc_final: 0.7611 (mtm) REVERT: E 216 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7226 (ptm160) REVERT: G 70 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6571 (t0) REVERT: G 93 LYS cc_start: 0.7114 (mttm) cc_final: 0.5348 (tttm) REVERT: G 102 MET cc_start: 0.5257 (tpt) cc_final: 0.4700 (tpt) REVERT: G 173 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5560 (mm-30) REVERT: G 174 ILE cc_start: 0.7455 (mt) cc_final: 0.7175 (mp) REVERT: G 216 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7391 (ptm160) REVERT: H 173 GLU cc_start: 0.6416 (tp30) cc_final: 0.5770 (tp30) REVERT: H 197 LEU cc_start: 0.6958 (mp) cc_final: 0.6603 (mt) REVERT: H 213 MET cc_start: 0.8087 (mtp) cc_final: 0.7687 (mtm) REVERT: I 93 LYS cc_start: 0.7213 (mttm) cc_final: 0.5505 (tttm) REVERT: I 173 GLU cc_start: 0.6212 (tp30) cc_final: 0.5615 (tp30) REVERT: I 195 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6956 (pt0) REVERT: I 219 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6786 (mt0) REVERT: J 93 LYS cc_start: 0.7071 (mttm) cc_final: 0.5575 (tttm) REVERT: J 174 ILE cc_start: 0.7543 (mt) cc_final: 0.7163 (mp) REVERT: J 213 MET cc_start: 0.8176 (mtp) cc_final: 0.7956 (mtm) REVERT: J 216 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6844 (ptm160) REVERT: J 219 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6919 (mt0) REVERT: J 223 SER cc_start: 0.8807 (m) cc_final: 0.8582 (m) REVERT: F 102 MET cc_start: 0.5810 (tpt) cc_final: 0.5001 (tpt) REVERT: F 118 ASN cc_start: 0.6932 (OUTLIER) cc_final: 0.6246 (t0) REVERT: F 173 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5551 (mm-30) REVERT: F 174 ILE cc_start: 0.7683 (mt) cc_final: 0.7322 (mp) REVERT: F 216 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6386 (ptm160) REVERT: F 219 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6601 (mt0) REVERT: D 102 MET cc_start: 0.5355 (tpt) cc_final: 0.4702 (tpt) REVERT: D 173 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5286 (mm-30) REVERT: D 174 ILE cc_start: 0.7372 (mt) cc_final: 0.7041 (mp) REVERT: D 216 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7353 (ptm160) REVERT: D 219 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6383 (mt0) REVERT: M 23 GLN cc_start: 0.6919 (mt0) cc_final: 0.6600 (mt0) REVERT: M 50 ASP cc_start: 0.7564 (m-30) cc_final: 0.7266 (t70) REVERT: P 50 ASP cc_start: 0.7419 (t70) cc_final: 0.7122 (t70) REVERT: T 36 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7678 (tptm) outliers start: 119 outliers final: 55 residues processed: 469 average time/residue: 0.6588 time to fit residues: 350.5864 Evaluate side-chains 483 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 407 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 36 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 0.1980 chunk 245 optimal weight: 0.4980 chunk 253 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 145 optimal weight: 0.0470 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 188 GLN B 180 GLN B 188 GLN C 188 GLN E 118 ASN E 143 HIS E 188 GLN G 118 ASN G 188 GLN H 118 ASN H 188 GLN I 118 ASN I 188 GLN J 188 GLN F 188 GLN D 118 ASN D 188 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.215051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.195074 restraints weight = 21449.340| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.33 r_work: 0.4147 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21880 Z= 0.098 Angle : 0.535 7.237 29570 Z= 0.275 Chirality : 0.046 0.159 3350 Planarity : 0.004 0.041 3710 Dihedral : 8.589 59.956 3270 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.66 % Allowed : 14.96 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2610 helix: 0.23 (0.17), residues: 1010 sheet: 0.88 (0.22), residues: 590 loop : -0.94 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 66 TYR 0.022 0.001 TYR G 75 PHE 0.013 0.001 PHE H 148 TRP 0.008 0.001 TRP T 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21850) covalent geometry : angle 0.53521 / 0.27 (29570) hydrogen bonds : bond 0.03320 / 2.16 ( 501) hydrogen bonds : angle 4.71055 / 3.32 ( 1443) metal coordination : bond 0.00622 / 0.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 406 time to evaluate : 0.850 Fit side-chains REVERT: A 93 LYS cc_start: 0.7150 (mttm) cc_final: 0.5583 (tttm) REVERT: A 173 GLU cc_start: 0.6218 (tp30) cc_final: 0.5630 (tp30) REVERT: B 93 LYS cc_start: 0.7180 (mttm) cc_final: 0.5643 (tttm) REVERT: B 216 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6732 (ptm160) REVERT: C 102 MET cc_start: 0.5776 (tpt) cc_final: 0.4855 (tpt) REVERT: C 173 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5395 (mm-30) REVERT: C 174 ILE cc_start: 0.7715 (mt) cc_final: 0.7375 (mp) REVERT: C 215 MET cc_start: 0.7978 (mtp) cc_final: 0.7623 (mtm) REVERT: C 216 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6736 (ptm160) REVERT: C 219 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6764 (mt0) REVERT: E 70 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6576 (t0) REVERT: E 140 MET cc_start: 0.8397 (tpt) cc_final: 0.8114 (mmp) REVERT: E 174 ILE cc_start: 0.7447 (mt) cc_final: 0.7075 (mp) REVERT: E 213 MET cc_start: 0.8033 (mtp) cc_final: 0.7721 (mtm) REVERT: E 216 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: E 219 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: G 93 LYS cc_start: 0.7171 (mttm) cc_final: 0.5437 (tttm) REVERT: G 102 MET cc_start: 0.5155 (tpt) cc_final: 0.4601 (tpt) REVERT: G 173 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5525 (mm-30) REVERT: G 174 ILE cc_start: 0.7470 (mt) cc_final: 0.7204 (mp) REVERT: G 216 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7393 (ptm160) REVERT: H 173 GLU cc_start: 0.6486 (tp30) cc_final: 0.5821 (tp30) REVERT: H 197 LEU cc_start: 0.6980 (mp) cc_final: 0.6625 (mt) REVERT: H 213 MET cc_start: 0.8082 (mtp) cc_final: 0.7700 (mtm) REVERT: I 93 LYS cc_start: 0.7293 (mttm) cc_final: 0.5600 (tttm) REVERT: I 173 GLU cc_start: 0.6222 (tp30) cc_final: 0.5624 (tp30) REVERT: I 195 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7005 (pt0) REVERT: I 211 MET cc_start: 0.7446 (tpp) cc_final: 0.7169 (mmt) REVERT: I 219 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: J 93 LYS cc_start: 0.7126 (mttm) cc_final: 0.5638 (tttm) REVERT: J 174 ILE cc_start: 0.7553 (mt) cc_final: 0.7184 (mp) REVERT: J 213 MET cc_start: 0.8179 (mtp) cc_final: 0.7961 (mtm) REVERT: J 219 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: J 223 SER cc_start: 0.8747 (m) cc_final: 0.8521 (m) REVERT: F 102 MET cc_start: 0.5822 (tpt) cc_final: 0.5020 (tpt) REVERT: F 118 ASN cc_start: 0.6919 (t0) cc_final: 0.6092 (t0) REVERT: F 173 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5572 (mm-30) REVERT: F 174 ILE cc_start: 0.7687 (mt) cc_final: 0.7360 (mp) REVERT: F 215 MET cc_start: 0.7872 (mtp) cc_final: 0.7310 (mtp) REVERT: F 216 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6516 (ptm160) REVERT: F 219 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: F 239 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.6964 (mmmt) REVERT: D 102 MET cc_start: 0.5429 (tpt) cc_final: 0.4806 (tpt) REVERT: D 173 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5270 (mm-30) REVERT: D 174 ILE cc_start: 0.7365 (mt) cc_final: 0.7058 (mp) REVERT: D 219 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: M 23 GLN cc_start: 0.6945 (mt0) cc_final: 0.6671 (mt0) REVERT: M 50 ASP cc_start: 0.7539 (m-30) cc_final: 0.7306 (t70) REVERT: O 13 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5726 (mp0) REVERT: P 50 ASP cc_start: 0.7429 (t70) cc_final: 0.7145 (t70) REVERT: S 1 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.5181 (ppp) outliers start: 109 outliers final: 59 residues processed: 451 average time/residue: 0.6651 time to fit residues: 339.9714 Evaluate side-chains 478 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 400 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 188 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 chunk 80 optimal weight: 0.0060 chunk 126 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 188 GLN B 188 GLN C 118 ASN C 188 GLN E 118 ASN E 143 HIS E 188 GLN E 222 ASN G 118 ASN G 188 GLN H 118 ASN H 188 GLN I 118 ASN I 188 GLN J 188 GLN F 188 GLN D 118 ASN D 188 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN M 75 GLN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.211132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190740 restraints weight = 21642.944| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.34 r_work: 0.4111 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21880 Z= 0.158 Angle : 0.613 10.312 29570 Z= 0.312 Chirality : 0.049 0.201 3350 Planarity : 0.004 0.043 3710 Dihedral : 9.198 59.149 3270 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.83 % Allowed : 15.04 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2610 helix: 0.13 (0.17), residues: 1020 sheet: 0.19 (0.19), residues: 700 loop : -1.04 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 66 TYR 0.017 0.002 TYR H 175 PHE 0.014 0.002 PHE J 148 TRP 0.013 0.002 TRP P 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (21850) covalent geometry : angle 0.61276 / 0.31 (29570) hydrogen bonds : bond 0.04090 / 2.66 ( 501) hydrogen bonds : angle 4.92129 / 3.45 ( 1443) metal coordination : bond 0.00824 / 0.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 407 time to evaluate : 0.954 Fit side-chains REVERT: A 93 LYS cc_start: 0.7156 (mttm) cc_final: 0.5561 (tttm) REVERT: B 93 LYS cc_start: 0.7189 (mttm) cc_final: 0.5649 (tttm) REVERT: B 216 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6674 (ptm160) REVERT: B 219 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: C 102 MET cc_start: 0.5800 (tpt) cc_final: 0.4877 (tpt) REVERT: C 173 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5487 (mt-10) REVERT: C 174 ILE cc_start: 0.7756 (mt) cc_final: 0.7386 (mp) REVERT: C 215 MET cc_start: 0.7997 (mtp) cc_final: 0.7619 (mtm) REVERT: C 216 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6666 (ptm160) REVERT: C 219 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: E 70 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6569 (t0) REVERT: E 93 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7057 (mttt) REVERT: E 213 MET cc_start: 0.8131 (mtp) cc_final: 0.7756 (mtm) REVERT: E 216 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7652 (ptm-80) REVERT: E 219 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: G 93 LYS cc_start: 0.7183 (mttm) cc_final: 0.5408 (tttm) REVERT: G 102 MET cc_start: 0.5275 (tpt) cc_final: 0.4677 (tpt) REVERT: G 173 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5511 (mm-30) REVERT: G 174 ILE cc_start: 0.7520 (mt) cc_final: 0.7192 (mp) REVERT: G 216 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7528 (ptm160) REVERT: G 219 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6639 (mt0) REVERT: H 102 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4568 (tpt) REVERT: H 211 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7465 (mtt) REVERT: H 213 MET cc_start: 0.8133 (mtp) cc_final: 0.7768 (mtm) REVERT: I 93 LYS cc_start: 0.7211 (mttm) cc_final: 0.5529 (tttm) REVERT: I 195 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6951 (pt0) REVERT: I 216 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7446 (ptm160) REVERT: I 219 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: I 221 MET cc_start: 0.5956 (ptp) cc_final: 0.5716 (ptp) REVERT: J 93 LYS cc_start: 0.7079 (mttm) cc_final: 0.5621 (tttm) REVERT: J 174 ILE cc_start: 0.7602 (mt) cc_final: 0.7175 (mp) REVERT: J 213 MET cc_start: 0.8225 (mtp) cc_final: 0.8017 (mtm) REVERT: J 216 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6730 (ptm160) REVERT: J 223 SER cc_start: 0.8826 (m) cc_final: 0.8595 (m) REVERT: F 102 MET cc_start: 0.5871 (tpt) cc_final: 0.5061 (tpt) REVERT: F 173 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5404 (mm-30) REVERT: F 215 MET cc_start: 0.7981 (mtp) cc_final: 0.7449 (mtp) REVERT: F 216 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6448 (ptm160) REVERT: F 239 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6990 (mmmt) REVERT: D 102 MET cc_start: 0.5383 (tpt) cc_final: 0.4742 (tpt) REVERT: D 173 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5313 (mm-30) REVERT: D 174 ILE cc_start: 0.7540 (mt) cc_final: 0.7198 (mp) REVERT: D 216 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7435 (ptm160) REVERT: D 219 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6399 (mt0) REVERT: D 239 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7234 (mmpt) REVERT: N 50 ASP cc_start: 0.7470 (m-30) cc_final: 0.7180 (t70) REVERT: M 23 GLN cc_start: 0.7000 (mt0) cc_final: 0.6749 (mt0) REVERT: M 50 ASP cc_start: 0.7558 (m-30) cc_final: 0.7291 (t70) REVERT: O 13 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: P 50 ASP cc_start: 0.7527 (t70) cc_final: 0.7234 (t70) outliers start: 113 outliers final: 55 residues processed: 457 average time/residue: 0.6687 time to fit residues: 345.7362 Evaluate side-chains 480 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 400 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 144 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 118 ASN C 188 GLN E 110 GLN E 118 ASN E 188 GLN G 118 ASN H 118 ASN H 188 GLN I 118 ASN I 188 GLN J 188 GLN F 110 GLN F 118 ASN F 188 GLN D 118 ASN D 188 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.210535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190077 restraints weight = 21713.288| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.33 r_work: 0.4103 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21880 Z= 0.163 Angle : 0.621 9.726 29570 Z= 0.317 Chirality : 0.049 0.227 3350 Planarity : 0.004 0.045 3710 Dihedral : 9.285 59.713 3270 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.44 % Allowed : 15.51 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2610 helix: 0.10 (0.17), residues: 1020 sheet: 0.10 (0.19), residues: 700 loop : -1.08 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 66 TYR 0.035 0.002 TYR I 75 PHE 0.015 0.002 PHE C 148 TRP 0.026 0.002 TRP M 79 HIS 0.008 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (21850) covalent geometry : angle 0.62082 / 0.32 (29570) hydrogen bonds : bond 0.04146 / 2.70 ( 501) hydrogen bonds : angle 5.01732 / 3.52 ( 1443) metal coordination : bond 0.00915 / 0.58 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 410 time to evaluate : 0.867 Fit side-chains REVERT: A 93 LYS cc_start: 0.7266 (mttm) cc_final: 0.5699 (tttm) REVERT: B 93 LYS cc_start: 0.7248 (mttm) cc_final: 0.5731 (tttm) REVERT: B 216 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6647 (ptm160) REVERT: C 102 MET cc_start: 0.5828 (tpt) cc_final: 0.4989 (tpp) REVERT: C 173 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5641 (mt-10) REVERT: C 174 ILE cc_start: 0.7754 (mt) cc_final: 0.7394 (mp) REVERT: C 215 MET cc_start: 0.8055 (mtp) cc_final: 0.7675 (mtm) REVERT: C 216 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6700 (ptm160) REVERT: C 219 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6830 (mt0) REVERT: E 70 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.6592 (t0) REVERT: E 93 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7120 (mttt) REVERT: E 102 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.4903 (tpt) REVERT: E 140 MET cc_start: 0.8407 (tpt) cc_final: 0.8033 (mmm) REVERT: E 213 MET cc_start: 0.8136 (mtp) cc_final: 0.7796 (mtm) REVERT: E 216 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7303 (ptm160) REVERT: E 219 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: G 93 LYS cc_start: 0.7246 (mttm) cc_final: 0.5497 (tttm) REVERT: G 102 MET cc_start: 0.5294 (tpt) cc_final: 0.4657 (tpt) REVERT: G 173 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5366 (mm-30) REVERT: G 174 ILE cc_start: 0.7609 (mt) cc_final: 0.7304 (mp) REVERT: G 216 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: G 219 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6671 (mt0) REVERT: H 102 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4639 (tpt) REVERT: H 197 LEU cc_start: 0.7115 (mp) cc_final: 0.6724 (mt) REVERT: H 211 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: H 213 MET cc_start: 0.8116 (mtp) cc_final: 0.7726 (mtm) REVERT: H 216 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7128 (ptm-80) REVERT: I 93 LYS cc_start: 0.7300 (mttm) cc_final: 0.5668 (tttm) REVERT: I 195 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6946 (pt0) REVERT: I 216 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7444 (ptm160) REVERT: I 219 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: I 221 MET cc_start: 0.5965 (ptp) cc_final: 0.5743 (ptp) REVERT: J 93 LYS cc_start: 0.7196 (mttm) cc_final: 0.5709 (tttm) REVERT: J 174 ILE cc_start: 0.7622 (mt) cc_final: 0.7203 (mp) REVERT: J 213 MET cc_start: 0.8261 (mtp) cc_final: 0.8060 (mtm) REVERT: J 216 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6729 (ptm160) REVERT: J 223 SER cc_start: 0.8830 (m) cc_final: 0.8595 (m) REVERT: F 102 MET cc_start: 0.5919 (tpt) cc_final: 0.5086 (tpt) REVERT: F 110 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7662 (mp10) REVERT: F 173 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5467 (mt-10) REVERT: F 215 MET cc_start: 0.7963 (mtp) cc_final: 0.7360 (mtp) REVERT: F 216 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6500 (ptm160) REVERT: F 219 GLN cc_start: 0.7246 (mt0) cc_final: 0.6833 (mt0) REVERT: F 239 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7026 (mmmt) REVERT: D 102 MET cc_start: 0.5411 (tpt) cc_final: 0.4770 (tpt) REVERT: D 173 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5353 (mm-30) REVERT: D 174 ILE cc_start: 0.7491 (mt) cc_final: 0.7161 (mp) REVERT: D 215 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: D 216 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7506 (ptm160) REVERT: D 219 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6621 (mt0) REVERT: D 239 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7245 (mmpt) REVERT: N 50 ASP cc_start: 0.7535 (m-30) cc_final: 0.7208 (t70) REVERT: M 23 GLN cc_start: 0.7107 (mt0) cc_final: 0.6717 (mt0) REVERT: O 13 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: P 50 ASP cc_start: 0.7312 (t70) cc_final: 0.7058 (t70) outliers start: 104 outliers final: 53 residues processed: 457 average time/residue: 0.6590 time to fit residues: 340.1416 Evaluate side-chains 481 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 401 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 214 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 118 ASN C 188 GLN E 110 GLN E 118 ASN E 188 GLN G 118 ASN G 188 GLN H 110 GLN H 188 GLN I 110 GLN I 118 ASN I 188 GLN J 188 GLN F 118 ASN F 188 GLN D 118 ASN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189971 restraints weight = 21807.176| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.33 r_work: 0.4099 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21880 Z= 0.163 Angle : 0.631 9.957 29570 Z= 0.321 Chirality : 0.049 0.188 3350 Planarity : 0.004 0.042 3710 Dihedral : 9.297 59.254 3270 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.27 % Allowed : 15.90 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2610 helix: 0.11 (0.17), residues: 1020 sheet: 0.08 (0.20), residues: 700 loop : -1.12 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 66 TYR 0.018 0.002 TYR H 175 PHE 0.015 0.002 PHE C 148 TRP 0.018 0.002 TRP P 79 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (21850) covalent geometry : angle 0.63125 / 0.32 (29570) hydrogen bonds : bond 0.04125 / 2.68 ( 501) hydrogen bonds : angle 5.00997 / 3.52 ( 1443) metal coordination : bond 0.00855 / 0.55 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8402.39 seconds wall clock time: 143 minutes 26.55 seconds (8606.55 seconds total)