Starting phenix.real_space_refine on Sun Nov 17 08:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp8_36471/11_2024/8jp8_36471.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 36 5.16 5 C 8466 2.51 5 N 2346 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.36, per 1000 atoms: 0.62 Number of scatterers: 13500 At special positions: 0 Unit cell: (119.52, 116.532, 128.484, 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 4 29.99 Ca 16 19.99 S 36 16.00 O 2632 8.00 N 2346 7.00 C 8466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 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: 3.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 32.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.736A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.761A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.175A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.944A pdb=" N ASN A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.512A pdb=" N ASN B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.606A pdb=" N LYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 362 removed outlier: 3.540A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.707A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.512A pdb=" N ASP C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.562A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.735A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.760A pdb=" N LYS E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 4.182A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 364 removed outlier: 3.987A pdb=" N ASN E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 364 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.514A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 181' Processing helix chain 'F' and resid 282 through 309 removed outlier: 3.607A pdb=" N LYS F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 362 removed outlier: 3.595A pdb=" N ARG F 361 " --> pdb=" O ASP F 357 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.706A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.560A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 137 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.587A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.742A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.587A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.742A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 202 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE A 229 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.705A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.705A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 249 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 122 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 123 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.661A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.502A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.661A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.502A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 261 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.754A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.754A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 249 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 122 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.578A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.828A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.578A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.828A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 202 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.710A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.710A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA E 249 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY E 122 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 123 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.640A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.553A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.640A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.553A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 261 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.690A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.690A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA F 249 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY F 122 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1866 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: 4.22 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4627 1.35 - 1.47: 3096 1.47 - 1.59: 6007 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" N ILE B 125 " pdb=" CA ILE B 125 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.67e+00 bond pdb=" N LEU A 133 " pdb=" CA LEU A 133 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N GLU E 134 " pdb=" CA GLU E 134 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.58e+00 bond pdb=" N GLU A 134 " pdb=" CA GLU A 134 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.49e+00 bond pdb=" N LEU E 133 " pdb=" CA LEU E 133 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.36e+00 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 18471 2.28 - 4.57: 138 4.57 - 6.85: 15 6.85 - 9.13: 3 9.13 - 11.41: 3 Bond angle restraints: 18630 Sorted by residual: angle pdb=" CB MET B 354 " pdb=" CG MET B 354 " pdb=" SD MET B 354 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C ILE F 125 " pdb=" N TRP F 126 " pdb=" CA TRP F 126 " ideal model delta sigma weight residual 122.74 117.27 5.47 1.54e+00 4.22e-01 1.26e+01 angle pdb=" N TRP B 126 " pdb=" CA TRP B 126 " pdb=" C TRP B 126 " ideal model delta sigma weight residual 109.24 114.53 -5.29 1.67e+00 3.59e-01 1.00e+01 angle pdb=" CA GLN A 131 " pdb=" C GLN A 131 " pdb=" O GLN A 131 " ideal model delta sigma weight residual 121.02 117.46 3.56 1.15e+00 7.56e-01 9.57e+00 angle pdb=" N TRP F 126 " pdb=" CA TRP F 126 " pdb=" C TRP F 126 " ideal model delta sigma weight residual 108.76 113.94 -5.18 1.69e+00 3.50e-01 9.38e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7191 17.13 - 34.26: 787 34.26 - 51.40: 165 51.40 - 68.53: 84 68.53 - 85.66: 21 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA TRP E 126 " pdb=" C TRP E 126 " pdb=" N TYR E 127 " pdb=" CA TYR E 127 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -118.92 32.92 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS F 190 " pdb=" SG CYS F 190 " pdb=" SG CYS F 230 " pdb=" CB CYS F 230 " ideal model delta sinusoidal sigma weight residual -86.00 -118.86 32.86 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1299 0.037 - 0.075: 431 0.075 - 0.112: 128 0.112 - 0.149: 51 0.149 - 0.186: 7 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA GLN A 131 " pdb=" N GLN A 131 " pdb=" C GLN A 131 " pdb=" CB GLN A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA GLN E 131 " pdb=" N GLN E 131 " pdb=" C GLN E 131 " pdb=" CB GLN E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 130 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ASN A 130 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN A 130 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 131 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 130 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN E 130 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN E 130 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN E 131 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 124 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ALA B 124 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA B 124 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 125 " 0.008 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 137 2.40 - 3.02: 7135 3.02 - 3.65: 20334 3.65 - 4.27: 30011 4.27 - 4.90: 51959 Nonbonded interactions: 109576 Sorted by model distance: nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 162 " model vdw 1.774 3.040 nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.778 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 162 " model vdw 1.822 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.834 3.040 nonbonded pdb=" CD2 HIS H 101 " pdb="ZN ZN H 703 " model vdw 1.971 2.450 ... (remaining 109571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.050 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.002 0.035 13794 Z= 0.144 Angle : 0.516 11.414 18630 Z= 0.279 Chirality : 0.044 0.186 1916 Planarity : 0.003 0.031 2510 Dihedral : 16.263 85.662 5140 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.07 % Allowed : 12.72 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1650 helix: 1.46 (0.23), residues: 492 sheet: 0.73 (0.30), residues: 364 loop : -1.02 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 126 HIS 0.007 0.001 HIS H 55 PHE 0.013 0.001 PHE E 52 TYR 0.012 0.001 TYR D 76 ARG 0.005 0.000 ARG E 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9165 (mm) cc_final: 0.8945 (mm) REVERT: A 218 ASN cc_start: 0.6771 (t0) cc_final: 0.6429 (p0) REVERT: A 226 ASP cc_start: 0.7509 (t70) cc_final: 0.7238 (t0) REVERT: A 297 GLN cc_start: 0.9236 (mt0) cc_final: 0.8875 (mt0) REVERT: A 349 ASN cc_start: 0.8430 (t0) cc_final: 0.8094 (t0) REVERT: B 77 SER cc_start: 0.8867 (m) cc_final: 0.8584 (t) REVERT: B 297 GLN cc_start: 0.8802 (pt0) cc_final: 0.8254 (pt0) REVERT: C 70 GLN cc_start: 0.8977 (pp30) cc_final: 0.8066 (pp30) REVERT: C 71 GLU cc_start: 0.8978 (tp30) cc_final: 0.8477 (tp30) REVERT: C 73 GLN cc_start: 0.8596 (pt0) cc_final: 0.8352 (pp30) REVERT: C 81 ASP cc_start: 0.8214 (t70) cc_final: 0.8003 (t0) REVERT: C 127 ASP cc_start: 0.8121 (m-30) cc_final: 0.7898 (m-30) REVERT: C 132 ASN cc_start: 0.8882 (t0) cc_final: 0.8466 (t0) REVERT: D 49 GLN cc_start: 0.8917 (tp-100) cc_final: 0.7654 (tp-100) REVERT: D 53 MET cc_start: 0.8935 (mmm) cc_final: 0.8524 (mmp) REVERT: D 86 ASN cc_start: 0.7824 (m-40) cc_final: 0.7143 (t0) REVERT: D 132 ASN cc_start: 0.8031 (t0) cc_final: 0.7692 (t0) REVERT: E 218 ASN cc_start: 0.7090 (t0) cc_final: 0.6790 (m110) REVERT: E 295 HIS cc_start: 0.9173 (t-90) cc_final: 0.8836 (t-90) REVERT: F 207 TYR cc_start: 0.8711 (t80) cc_final: 0.8460 (t80) REVERT: F 223 ASP cc_start: 0.7926 (t0) cc_final: 0.7655 (t0) REVERT: G 49 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8347 (tp-100) REVERT: H 78 LYS cc_start: 0.9294 (tptt) cc_final: 0.9046 (tppt) REVERT: H 132 ASN cc_start: 0.8790 (t0) cc_final: 0.8413 (t0) REVERT: H 135 TYR cc_start: 0.7824 (m-80) cc_final: 0.7136 (m-80) outliers start: 1 outliers final: 1 residues processed: 398 average time/residue: 0.2844 time to fit residues: 158.0305 Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 235 ASN A 257 HIS A 351 GLN B 241 GLN B 311 HIS B 333 GLN B 342 HIS B 359 GLN C 70 GLN C 75 HIS C 80 HIS C 86 ASN D 55 HIS D 80 HIS D 101 HIS E 43 HIS E 59 GLN E 79 GLN E 257 HIS E 342 HIS E 351 GLN F 191 GLN F 235 ASN F 241 GLN F 333 GLN G 70 GLN G 73 GLN G 80 HIS H 73 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13794 Z= 0.270 Angle : 0.574 11.538 18630 Z= 0.304 Chirality : 0.046 0.204 1916 Planarity : 0.004 0.066 2510 Dihedral : 4.282 57.844 1790 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.42 % Allowed : 17.08 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1650 helix: 1.68 (0.23), residues: 506 sheet: 0.50 (0.29), residues: 360 loop : -0.99 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 126 HIS 0.012 0.001 HIS C 80 PHE 0.023 0.002 PHE E 323 TYR 0.024 0.002 TYR D 76 ARG 0.007 0.001 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9284 (mm) cc_final: 0.9025 (mm) REVERT: A 218 ASN cc_start: 0.6918 (t0) cc_final: 0.6500 (p0) REVERT: A 226 ASP cc_start: 0.7648 (t70) cc_final: 0.7382 (t0) REVERT: A 349 ASN cc_start: 0.8455 (t0) cc_final: 0.8100 (t0) REVERT: B 77 SER cc_start: 0.9012 (m) cc_final: 0.8676 (t) REVERT: B 223 ASP cc_start: 0.8032 (t0) cc_final: 0.7781 (t0) REVERT: B 224 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7635 (tptt) REVERT: C 70 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: C 73 GLN cc_start: 0.8699 (pt0) cc_final: 0.8380 (pp30) REVERT: C 94 SER cc_start: 0.9032 (t) cc_final: 0.8575 (p) REVERT: C 132 ASN cc_start: 0.8941 (t0) cc_final: 0.8564 (t0) REVERT: C 138 TYR cc_start: 0.8434 (t80) cc_final: 0.8063 (t80) REVERT: D 49 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8389 (tp-100) REVERT: D 77 PHE cc_start: 0.8432 (t80) cc_final: 0.8119 (t80) REVERT: D 113 SER cc_start: 0.8766 (t) cc_final: 0.8558 (t) REVERT: D 119 ASN cc_start: 0.8015 (m-40) cc_final: 0.7748 (m110) REVERT: D 132 ASN cc_start: 0.8001 (t0) cc_final: 0.7609 (t0) REVERT: E 171 ASN cc_start: 0.8922 (m110) cc_final: 0.8466 (t0) REVERT: E 199 TYR cc_start: 0.9095 (m-10) cc_final: 0.8885 (m-10) REVERT: E 258 ASP cc_start: 0.8332 (m-30) cc_final: 0.8015 (m-30) REVERT: F 223 ASP cc_start: 0.8026 (t0) cc_final: 0.7818 (t0) REVERT: F 289 TYR cc_start: 0.8858 (m-80) cc_final: 0.8581 (m-10) REVERT: F 340 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7456 (ttm-80) REVERT: G 47 HIS cc_start: 0.9204 (m-70) cc_final: 0.8584 (m-70) REVERT: G 75 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8314 (t-90) REVERT: G 92 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7042 (mt-10) REVERT: H 78 LYS cc_start: 0.9269 (tptt) cc_final: 0.8992 (tppt) REVERT: H 112 MET cc_start: 0.8046 (tpp) cc_final: 0.7691 (tpp) REVERT: H 132 ASN cc_start: 0.8812 (t0) cc_final: 0.8435 (t0) REVERT: H 135 TYR cc_start: 0.7860 (m-80) cc_final: 0.7142 (m-80) outliers start: 35 outliers final: 21 residues processed: 290 average time/residue: 0.2695 time to fit residues: 112.4017 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 75 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 297 GLN B 311 HIS C 73 GLN C 75 HIS C 80 HIS D 73 GLN E 43 HIS F 359 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN H 80 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13794 Z= 0.219 Angle : 0.556 12.659 18630 Z= 0.290 Chirality : 0.045 0.201 1916 Planarity : 0.004 0.079 2510 Dihedral : 4.230 53.784 1790 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.11 % Allowed : 17.57 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1650 helix: 1.74 (0.24), residues: 496 sheet: 0.44 (0.29), residues: 360 loop : -0.95 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.009 0.001 HIS D 55 PHE 0.024 0.002 PHE B 293 TYR 0.018 0.001 TYR D 76 ARG 0.004 0.000 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9278 (mm) cc_final: 0.9029 (mm) REVERT: A 218 ASN cc_start: 0.6878 (t0) cc_final: 0.6480 (p0) REVERT: A 224 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7805 (tptt) REVERT: A 349 ASN cc_start: 0.8402 (t0) cc_final: 0.8060 (t0) REVERT: B 77 SER cc_start: 0.8998 (m) cc_final: 0.8670 (t) REVERT: B 223 ASP cc_start: 0.8052 (t0) cc_final: 0.7686 (t0) REVERT: B 224 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7580 (tptt) REVERT: B 347 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 94 SER cc_start: 0.9055 (t) cc_final: 0.8650 (p) REVERT: C 132 ASN cc_start: 0.8945 (t0) cc_final: 0.8583 (t0) REVERT: D 49 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8826 (tp-100) REVERT: D 77 PHE cc_start: 0.8414 (t80) cc_final: 0.8117 (t80) REVERT: D 126 ARG cc_start: 0.8609 (ptp-110) cc_final: 0.8110 (ptp-110) REVERT: D 132 ASN cc_start: 0.8168 (t0) cc_final: 0.7756 (t0) REVERT: E 171 ASN cc_start: 0.8931 (m110) cc_final: 0.8398 (t0) REVERT: E 258 ASP cc_start: 0.8375 (m-30) cc_final: 0.8020 (m-30) REVERT: F 340 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7527 (ttm-80) REVERT: G 47 HIS cc_start: 0.9214 (m-70) cc_final: 0.8613 (m-70) REVERT: G 73 GLN cc_start: 0.8506 (pt0) cc_final: 0.8267 (pp30) REVERT: G 75 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (t-90) REVERT: G 92 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7152 (mt-10) REVERT: G 140 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6589 (mt-10) REVERT: H 62 LYS cc_start: 0.9042 (tttt) cc_final: 0.8813 (mmtm) REVERT: H 78 LYS cc_start: 0.9247 (tptt) cc_final: 0.8971 (tppt) REVERT: H 132 ASN cc_start: 0.8839 (t0) cc_final: 0.8434 (t0) REVERT: H 135 TYR cc_start: 0.7939 (m-80) cc_final: 0.7223 (m-80) REVERT: H 143 LYS cc_start: 0.8952 (tppt) cc_final: 0.8622 (tppt) outliers start: 45 outliers final: 23 residues processed: 291 average time/residue: 0.2657 time to fit residues: 110.8985 Evaluate side-chains 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 311 HIS C 75 HIS C 86 ASN F 191 GLN F 235 ASN G 49 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13794 Z= 0.407 Angle : 0.630 13.278 18630 Z= 0.333 Chirality : 0.048 0.220 1916 Planarity : 0.004 0.076 2510 Dihedral : 4.572 53.581 1790 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.73 % Allowed : 18.46 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1650 helix: 1.42 (0.23), residues: 498 sheet: 0.25 (0.29), residues: 356 loop : -1.01 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 67 HIS 0.006 0.001 HIS F 342 PHE 0.024 0.002 PHE E 52 TYR 0.025 0.002 TYR C 138 ARG 0.003 0.000 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: A 218 ASN cc_start: 0.7055 (t0) cc_final: 0.6534 (p0) REVERT: A 224 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7805 (tptt) REVERT: A 258 ASP cc_start: 0.8830 (m-30) cc_final: 0.8542 (m-30) REVERT: A 297 GLN cc_start: 0.9248 (mt0) cc_final: 0.9033 (mt0) REVERT: A 349 ASN cc_start: 0.8398 (t0) cc_final: 0.8030 (t0) REVERT: B 77 SER cc_start: 0.9127 (m) cc_final: 0.8873 (t) REVERT: B 223 ASP cc_start: 0.8139 (t0) cc_final: 0.7756 (t0) REVERT: B 224 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7482 (tptt) REVERT: B 347 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 94 SER cc_start: 0.9110 (t) cc_final: 0.8779 (p) REVERT: C 132 ASN cc_start: 0.9009 (t0) cc_final: 0.8663 (t0) REVERT: D 119 ASN cc_start: 0.7946 (m-40) cc_final: 0.7614 (m110) REVERT: D 126 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.8208 (ptp-110) REVERT: D 132 ASN cc_start: 0.8256 (t0) cc_final: 0.7972 (t0) REVERT: E 171 ASN cc_start: 0.8954 (m110) cc_final: 0.8388 (t0) REVERT: E 258 ASP cc_start: 0.8405 (m-30) cc_final: 0.7906 (m-30) REVERT: E 344 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7713 (mm-30) REVERT: G 47 HIS cc_start: 0.9224 (m-70) cc_final: 0.8649 (m-70) REVERT: G 49 GLN cc_start: 0.8529 (tp40) cc_final: 0.8022 (tp-100) REVERT: G 53 MET cc_start: 0.8736 (ptt) cc_final: 0.7834 (ptt) REVERT: G 75 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8377 (t-90) REVERT: G 132 ASN cc_start: 0.8216 (t0) cc_final: 0.7976 (t0) REVERT: G 140 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7284 (mt-10) REVERT: H 53 MET cc_start: 0.9139 (mmp) cc_final: 0.8713 (mmm) REVERT: H 62 LYS cc_start: 0.9086 (tttt) cc_final: 0.8830 (mmtm) REVERT: H 78 LYS cc_start: 0.9240 (tptt) cc_final: 0.8924 (tppt) REVERT: H 112 MET cc_start: 0.7939 (tpp) cc_final: 0.7650 (tpp) REVERT: H 116 GLU cc_start: 0.8275 (mp0) cc_final: 0.7837 (mp0) REVERT: H 132 ASN cc_start: 0.8800 (t0) cc_final: 0.8448 (t0) REVERT: H 135 TYR cc_start: 0.8036 (m-80) cc_final: 0.7235 (m-80) REVERT: H 143 LYS cc_start: 0.8961 (tppt) cc_final: 0.8628 (tppt) outliers start: 54 outliers final: 37 residues processed: 285 average time/residue: 0.2620 time to fit residues: 107.4919 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 136 optimal weight: 0.0070 chunk 110 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 308 GLN A 342 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS C 49 GLN C 75 HIS C 86 ASN E 43 HIS G 80 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13794 Z= 0.160 Angle : 0.566 13.437 18630 Z= 0.293 Chirality : 0.044 0.226 1916 Planarity : 0.003 0.056 2510 Dihedral : 4.238 50.994 1790 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.97 % Allowed : 20.12 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1650 helix: 1.70 (0.24), residues: 486 sheet: 0.47 (0.29), residues: 356 loop : -0.99 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.005 0.001 HIS D 80 PHE 0.036 0.001 PHE B 296 TYR 0.029 0.001 TYR C 138 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 218 ASN cc_start: 0.6804 (t0) cc_final: 0.6390 (p0) REVERT: A 258 ASP cc_start: 0.8630 (m-30) cc_final: 0.8296 (m-30) REVERT: A 349 ASN cc_start: 0.8390 (t0) cc_final: 0.8095 (t0) REVERT: B 77 SER cc_start: 0.9002 (m) cc_final: 0.8736 (t) REVERT: B 223 ASP cc_start: 0.8042 (t0) cc_final: 0.7668 (t0) REVERT: B 224 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7432 (tptt) REVERT: B 347 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 70 GLN cc_start: 0.9149 (pm20) cc_final: 0.8772 (pm20) REVERT: C 73 GLN cc_start: 0.8796 (pt0) cc_final: 0.8553 (pp30) REVERT: C 94 SER cc_start: 0.9047 (t) cc_final: 0.8803 (p) REVERT: C 132 ASN cc_start: 0.8927 (t0) cc_final: 0.8609 (t0) REVERT: D 67 MET cc_start: 0.7539 (tmm) cc_final: 0.6941 (pmm) REVERT: D 119 ASN cc_start: 0.7980 (m-40) cc_final: 0.7662 (m110) REVERT: D 126 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8318 (ptp-110) REVERT: D 132 ASN cc_start: 0.8205 (t0) cc_final: 0.7905 (t0) REVERT: E 171 ASN cc_start: 0.8967 (m110) cc_final: 0.8343 (t0) REVERT: E 258 ASP cc_start: 0.8327 (m-30) cc_final: 0.8039 (m-30) REVERT: E 344 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7693 (mm-30) REVERT: F 258 ASP cc_start: 0.8511 (m-30) cc_final: 0.8298 (m-30) REVERT: G 47 HIS cc_start: 0.9271 (m-70) cc_final: 0.8670 (m-70) REVERT: G 49 GLN cc_start: 0.8474 (tp40) cc_final: 0.8013 (tp-100) REVERT: G 53 MET cc_start: 0.8812 (ptt) cc_final: 0.8081 (ptt) REVERT: G 73 GLN cc_start: 0.8400 (pt0) cc_final: 0.8131 (pp30) REVERT: G 75 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8433 (t-90) REVERT: G 126 ARG cc_start: 0.8267 (tmm-80) cc_final: 0.8024 (tmm-80) REVERT: G 127 ASP cc_start: 0.8203 (m-30) cc_final: 0.7482 (m-30) REVERT: G 128 ASP cc_start: 0.8135 (m-30) cc_final: 0.7824 (m-30) REVERT: G 132 ASN cc_start: 0.8218 (t0) cc_final: 0.7901 (t0) REVERT: G 138 TYR cc_start: 0.7571 (t80) cc_final: 0.7200 (t80) REVERT: G 140 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6973 (mt-10) REVERT: H 53 MET cc_start: 0.9217 (mmp) cc_final: 0.8946 (mmm) REVERT: H 78 LYS cc_start: 0.9204 (tptt) cc_final: 0.8894 (tppt) REVERT: H 112 MET cc_start: 0.7899 (tpp) cc_final: 0.7664 (tpp) REVERT: H 116 GLU cc_start: 0.8163 (mp0) cc_final: 0.7963 (mp0) REVERT: H 132 ASN cc_start: 0.8803 (t0) cc_final: 0.8421 (t0) outliers start: 43 outliers final: 25 residues processed: 281 average time/residue: 0.2711 time to fit residues: 109.3096 Evaluate side-chains 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 311 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 131 GLN F 173 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN G 99 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13794 Z= 0.187 Angle : 0.580 14.952 18630 Z= 0.300 Chirality : 0.045 0.250 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.231 49.505 1790 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.04 % Allowed : 19.92 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1650 helix: 1.85 (0.24), residues: 460 sheet: 0.51 (0.29), residues: 346 loop : -0.92 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 126 HIS 0.007 0.001 HIS H 80 PHE 0.024 0.001 PHE B 293 TYR 0.026 0.002 TYR C 138 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8956 (pt0) REVERT: A 209 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 218 ASN cc_start: 0.6942 (t0) cc_final: 0.6495 (p0) REVERT: A 349 ASN cc_start: 0.8306 (t0) cc_final: 0.7987 (t0) REVERT: B 77 SER cc_start: 0.9030 (m) cc_final: 0.8756 (t) REVERT: B 223 ASP cc_start: 0.8070 (t0) cc_final: 0.7680 (t0) REVERT: B 224 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7420 (tptt) REVERT: C 49 GLN cc_start: 0.8728 (tp40) cc_final: 0.8513 (tp-100) REVERT: C 56 LEU cc_start: 0.9363 (tp) cc_final: 0.8975 (mt) REVERT: C 74 LEU cc_start: 0.8832 (mt) cc_final: 0.8548 (tt) REVERT: C 86 ASN cc_start: 0.8487 (m-40) cc_final: 0.8211 (t0) REVERT: C 132 ASN cc_start: 0.8928 (t0) cc_final: 0.8618 (t0) REVERT: D 53 MET cc_start: 0.8709 (mmm) cc_final: 0.8412 (mmm) REVERT: D 80 HIS cc_start: 0.8488 (m90) cc_final: 0.7807 (m90) REVERT: D 119 ASN cc_start: 0.8060 (m-40) cc_final: 0.7681 (m110) REVERT: D 126 ARG cc_start: 0.8643 (ptp-110) cc_final: 0.8290 (ptp-110) REVERT: D 132 ASN cc_start: 0.8221 (t0) cc_final: 0.7956 (t0) REVERT: E 171 ASN cc_start: 0.8898 (m110) cc_final: 0.8275 (t0) REVERT: F 258 ASP cc_start: 0.8525 (m-30) cc_final: 0.8297 (m-30) REVERT: F 289 TYR cc_start: 0.8886 (m-80) cc_final: 0.8649 (m-10) REVERT: G 47 HIS cc_start: 0.9268 (m-70) cc_final: 0.8430 (m-70) REVERT: G 49 GLN cc_start: 0.8329 (tp40) cc_final: 0.7951 (tp-100) REVERT: G 53 MET cc_start: 0.8797 (ptt) cc_final: 0.8291 (ptt) REVERT: G 73 GLN cc_start: 0.8479 (pt0) cc_final: 0.8164 (pp30) REVERT: G 75 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8452 (t-90) REVERT: G 132 ASN cc_start: 0.8237 (t0) cc_final: 0.7891 (t0) REVERT: G 140 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7046 (mt-10) REVERT: H 53 MET cc_start: 0.9220 (mmp) cc_final: 0.8634 (mmp) REVERT: H 70 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7527 (pp30) REVERT: H 78 LYS cc_start: 0.9264 (tptt) cc_final: 0.8924 (tppt) REVERT: H 86 ASN cc_start: 0.8767 (m-40) cc_final: 0.8560 (m-40) REVERT: H 116 GLU cc_start: 0.8233 (mp0) cc_final: 0.8010 (mp0) REVERT: H 132 ASN cc_start: 0.8788 (t0) cc_final: 0.8359 (t0) outliers start: 44 outliers final: 27 residues processed: 280 average time/residue: 0.2591 time to fit residues: 104.5901 Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN C 49 GLN C 75 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 191 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13794 Z= 0.325 Angle : 0.646 14.913 18630 Z= 0.337 Chirality : 0.048 0.254 1916 Planarity : 0.004 0.055 2510 Dihedral : 4.524 48.838 1790 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.39 % Allowed : 19.85 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1650 helix: 1.33 (0.24), residues: 486 sheet: 0.40 (0.29), residues: 340 loop : -1.07 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 67 HIS 0.008 0.001 HIS H 80 PHE 0.023 0.002 PHE B 293 TYR 0.026 0.002 TYR B 289 ARG 0.005 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: A 218 ASN cc_start: 0.6977 (t0) cc_final: 0.6504 (p0) REVERT: A 258 ASP cc_start: 0.8774 (m-30) cc_final: 0.8283 (m-30) REVERT: A 349 ASN cc_start: 0.8323 (t0) cc_final: 0.7926 (t0) REVERT: A 353 ASP cc_start: 0.8901 (m-30) cc_final: 0.8612 (m-30) REVERT: B 223 ASP cc_start: 0.8116 (t0) cc_final: 0.7725 (t0) REVERT: B 224 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7425 (tptt) REVERT: C 56 LEU cc_start: 0.9396 (tp) cc_final: 0.9019 (mt) REVERT: C 74 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 132 ASN cc_start: 0.9001 (t0) cc_final: 0.8708 (t0) REVERT: C 140 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7004 (mt-10) REVERT: D 53 MET cc_start: 0.8725 (mmm) cc_final: 0.8371 (mmp) REVERT: D 67 MET cc_start: 0.7392 (tmm) cc_final: 0.6954 (pmm) REVERT: D 119 ASN cc_start: 0.8074 (m-40) cc_final: 0.7711 (m110) REVERT: D 126 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8318 (ptp-110) REVERT: D 132 ASN cc_start: 0.8281 (t0) cc_final: 0.8064 (t0) REVERT: E 171 ASN cc_start: 0.8901 (m110) cc_final: 0.8260 (t0) REVERT: E 344 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7725 (mm-30) REVERT: F 289 TYR cc_start: 0.8926 (m-80) cc_final: 0.8631 (m-10) REVERT: G 47 HIS cc_start: 0.9088 (m-70) cc_final: 0.8470 (m-70) REVERT: G 73 GLN cc_start: 0.8524 (pt0) cc_final: 0.8240 (pp30) REVERT: G 75 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8432 (t-90) REVERT: G 132 ASN cc_start: 0.8223 (t0) cc_final: 0.8021 (t0) REVERT: G 140 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7132 (mt-10) REVERT: H 53 MET cc_start: 0.9228 (mmp) cc_final: 0.8841 (mmm) REVERT: H 78 LYS cc_start: 0.9151 (tptt) cc_final: 0.8720 (tppt) REVERT: H 132 ASN cc_start: 0.8778 (t0) cc_final: 0.8428 (t0) outliers start: 49 outliers final: 33 residues processed: 267 average time/residue: 0.2658 time to fit residues: 102.2133 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN H 80 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13794 Z= 0.261 Angle : 0.631 14.277 18630 Z= 0.331 Chirality : 0.047 0.248 1916 Planarity : 0.004 0.052 2510 Dihedral : 4.428 46.437 1790 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.18 % Allowed : 20.47 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1650 helix: 1.44 (0.24), residues: 474 sheet: 0.35 (0.29), residues: 350 loop : -1.00 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 126 HIS 0.005 0.001 HIS C 80 PHE 0.023 0.002 PHE B 293 TYR 0.029 0.002 TYR B 289 ARG 0.007 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8409 (t0) cc_final: 0.8197 (t0) REVERT: A 79 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: A 218 ASN cc_start: 0.6910 (t0) cc_final: 0.6480 (p0) REVERT: A 258 ASP cc_start: 0.8746 (m-30) cc_final: 0.8252 (m-30) REVERT: A 349 ASN cc_start: 0.8318 (t0) cc_final: 0.7997 (t0) REVERT: B 223 ASP cc_start: 0.8118 (t0) cc_final: 0.7707 (t0) REVERT: B 224 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7428 (tptt) REVERT: C 56 LEU cc_start: 0.9388 (tp) cc_final: 0.9031 (mt) REVERT: C 78 LYS cc_start: 0.8977 (tptp) cc_final: 0.8650 (tppt) REVERT: C 86 ASN cc_start: 0.8639 (m-40) cc_final: 0.8314 (t0) REVERT: C 94 SER cc_start: 0.9077 (t) cc_final: 0.8831 (p) REVERT: C 132 ASN cc_start: 0.8969 (t0) cc_final: 0.8659 (t0) REVERT: D 53 MET cc_start: 0.8828 (mmm) cc_final: 0.8488 (mmm) REVERT: D 67 MET cc_start: 0.7417 (tmm) cc_final: 0.7099 (pmm) REVERT: D 80 HIS cc_start: 0.8602 (m90) cc_final: 0.8314 (m-70) REVERT: D 119 ASN cc_start: 0.8076 (m-40) cc_final: 0.7723 (m110) REVERT: D 126 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8326 (ptp-110) REVERT: D 132 ASN cc_start: 0.8270 (t0) cc_final: 0.8061 (t0) REVERT: E 171 ASN cc_start: 0.8925 (m110) cc_final: 0.8250 (t0) REVERT: E 344 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7732 (mm-30) REVERT: E 354 MET cc_start: 0.8240 (tpp) cc_final: 0.7930 (tmm) REVERT: F 258 ASP cc_start: 0.8610 (m-30) cc_final: 0.8356 (m-30) REVERT: F 289 TYR cc_start: 0.8946 (m-80) cc_final: 0.8675 (m-10) REVERT: G 47 HIS cc_start: 0.8970 (m-70) cc_final: 0.8342 (m-70) REVERT: G 49 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8276 (tp-100) REVERT: G 73 GLN cc_start: 0.8436 (pt0) cc_final: 0.8160 (pp30) REVERT: G 75 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8446 (t-90) REVERT: G 140 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7111 (mt-10) REVERT: H 53 MET cc_start: 0.9235 (mmp) cc_final: 0.8845 (mmm) REVERT: H 70 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7626 (pp30) REVERT: H 78 LYS cc_start: 0.9181 (tptt) cc_final: 0.8722 (tppt) REVERT: H 132 ASN cc_start: 0.8771 (t0) cc_final: 0.8416 (t0) outliers start: 46 outliers final: 34 residues processed: 265 average time/residue: 0.2776 time to fit residues: 105.9674 Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS H 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13794 Z= 0.343 Angle : 0.658 13.657 18630 Z= 0.347 Chirality : 0.048 0.275 1916 Planarity : 0.004 0.057 2510 Dihedral : 4.521 45.541 1790 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.84 % Allowed : 20.75 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1650 helix: 1.21 (0.24), residues: 484 sheet: 0.24 (0.29), residues: 350 loop : -1.04 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 67 HIS 0.006 0.001 HIS H 80 PHE 0.023 0.002 PHE B 293 TYR 0.035 0.002 TYR B 289 ARG 0.009 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: A 258 ASP cc_start: 0.8771 (m-30) cc_final: 0.8513 (m-30) REVERT: A 349 ASN cc_start: 0.8309 (t0) cc_final: 0.7986 (t0) REVERT: B 223 ASP cc_start: 0.8140 (t0) cc_final: 0.7737 (t0) REVERT: B 224 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7426 (tptt) REVERT: C 56 LEU cc_start: 0.9388 (tp) cc_final: 0.9058 (mt) REVERT: C 73 GLN cc_start: 0.8881 (pt0) cc_final: 0.8623 (pp30) REVERT: C 78 LYS cc_start: 0.8978 (tptp) cc_final: 0.8635 (tppt) REVERT: C 86 ASN cc_start: 0.8665 (m-40) cc_final: 0.8338 (t0) REVERT: C 94 SER cc_start: 0.9093 (t) cc_final: 0.8831 (p) REVERT: C 130 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8024 (mtmt) REVERT: C 132 ASN cc_start: 0.9024 (t0) cc_final: 0.8727 (t0) REVERT: D 53 MET cc_start: 0.8849 (mmm) cc_final: 0.8484 (mmp) REVERT: D 67 MET cc_start: 0.7362 (tmm) cc_final: 0.7104 (pmm) REVERT: D 119 ASN cc_start: 0.8058 (m-40) cc_final: 0.7623 (m110) REVERT: D 126 ARG cc_start: 0.8680 (ptp-110) cc_final: 0.8318 (ptp-110) REVERT: E 43 HIS cc_start: 0.7052 (t70) cc_final: 0.6738 (t-90) REVERT: E 171 ASN cc_start: 0.8932 (m110) cc_final: 0.8244 (t0) REVERT: E 354 MET cc_start: 0.8294 (tpp) cc_final: 0.7960 (tmm) REVERT: F 289 TYR cc_start: 0.8951 (m-80) cc_final: 0.8722 (m-10) REVERT: G 47 HIS cc_start: 0.8997 (m-70) cc_final: 0.8261 (m-70) REVERT: G 49 GLN cc_start: 0.8602 (tp-100) cc_final: 0.7888 (tp-100) REVERT: G 126 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: G 132 ASN cc_start: 0.8260 (t0) cc_final: 0.7940 (t0) REVERT: G 140 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7198 (mt-10) REVERT: H 53 MET cc_start: 0.9239 (mmp) cc_final: 0.8851 (mmp) REVERT: H 70 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (pp30) REVERT: H 78 LYS cc_start: 0.9203 (tptt) cc_final: 0.8786 (tppt) REVERT: H 132 ASN cc_start: 0.8763 (t0) cc_final: 0.8422 (t0) outliers start: 41 outliers final: 35 residues processed: 255 average time/residue: 0.2632 time to fit residues: 96.3939 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 43 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13794 Z= 0.478 Angle : 0.729 16.743 18630 Z= 0.383 Chirality : 0.051 0.315 1916 Planarity : 0.005 0.069 2510 Dihedral : 4.769 44.893 1790 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 21.02 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1650 helix: 1.06 (0.24), residues: 482 sheet: 0.14 (0.29), residues: 342 loop : -1.18 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 67 HIS 0.012 0.001 HIS H 80 PHE 0.028 0.002 PHE E 52 TYR 0.039 0.002 TYR B 289 ARG 0.007 0.001 ARG B 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: A 218 ASN cc_start: 0.7328 (t0) cc_final: 0.6643 (p0) REVERT: A 258 ASP cc_start: 0.8832 (m-30) cc_final: 0.8498 (m-30) REVERT: A 349 ASN cc_start: 0.8388 (t0) cc_final: 0.8031 (t0) REVERT: B 223 ASP cc_start: 0.8156 (t0) cc_final: 0.7765 (t0) REVERT: B 224 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7423 (tptt) REVERT: C 56 LEU cc_start: 0.9394 (tp) cc_final: 0.9076 (mt) REVERT: C 78 LYS cc_start: 0.9031 (tptp) cc_final: 0.8714 (tppt) REVERT: C 130 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8112 (mtmt) REVERT: C 132 ASN cc_start: 0.9111 (t0) cc_final: 0.8825 (t0) REVERT: D 53 MET cc_start: 0.8875 (mmm) cc_final: 0.8487 (mmp) REVERT: D 119 ASN cc_start: 0.8076 (m-40) cc_final: 0.7638 (m110) REVERT: D 126 ARG cc_start: 0.8725 (ptp-110) cc_final: 0.8314 (ptp-110) REVERT: E 171 ASN cc_start: 0.8932 (m110) cc_final: 0.8237 (t0) REVERT: E 258 ASP cc_start: 0.8267 (m-30) cc_final: 0.7719 (m-30) REVERT: E 354 MET cc_start: 0.8299 (tpp) cc_final: 0.7976 (tmm) REVERT: G 47 HIS cc_start: 0.9013 (m-70) cc_final: 0.8302 (m-70) REVERT: G 73 GLN cc_start: 0.8543 (pt0) cc_final: 0.8184 (pp30) REVERT: G 140 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6970 (mt-10) REVERT: H 53 MET cc_start: 0.9265 (mmp) cc_final: 0.8895 (mmp) REVERT: H 78 LYS cc_start: 0.9141 (tptt) cc_final: 0.8741 (tppt) REVERT: H 132 ASN cc_start: 0.8762 (t0) cc_final: 0.8468 (t0) outliers start: 40 outliers final: 36 residues processed: 259 average time/residue: 0.2680 time to fit residues: 99.7394 Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 191 GLN F 342 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112539 restraints weight = 19707.493| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.97 r_work: 0.3135 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13794 Z= 0.202 Angle : 0.679 16.183 18630 Z= 0.353 Chirality : 0.047 0.302 1916 Planarity : 0.004 0.048 2510 Dihedral : 4.407 42.507 1790 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.28 % Allowed : 22.27 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1650 helix: 1.21 (0.24), residues: 478 sheet: 0.33 (0.29), residues: 350 loop : -1.10 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 126 HIS 0.008 0.001 HIS H 80 PHE 0.022 0.001 PHE B 293 TYR 0.034 0.002 TYR B 289 ARG 0.011 0.000 ARG B 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.79 seconds wall clock time: 56 minutes 36.36 seconds (3396.36 seconds total)