Starting phenix.real_space_refine on Sun Nov 17 08:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp9_36472/11_2024/8jp9_36472.cif" } resolution = 3.37 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= 0.113 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 2 residue(s): 0.03s 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: 8.49, per 1000 atoms: 0.63 Number of scatterers: 13500 At special positions: 0 Unit cell: (120.516, 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: 3.14 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: 41 helices and 16 sheets defined 32.7% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.646A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.728A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.095A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.799A pdb=" N ASN A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.816A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.714A pdb=" N LYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 361 removed outlier: 3.589A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.512A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.508A 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 57 Processing helix chain 'D' and resid 68 through 81 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 48 through 51 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.556A pdb=" N ASN E 180 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 181' Processing helix chain 'E' and resid 282 through 309 removed outlier: 4.102A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 362 removed outlier: 3.818A pdb=" N ASN E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.577A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.709A pdb=" N LYS F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 361 removed outlier: 3.581A pdb=" N ARG F 361 " --> pdb=" O ASP F 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.514A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.553A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) 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 57 Processing helix chain 'H' and resid 68 through 81 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 46 removed outlier: 6.946A 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 46 removed outlier: 5.593A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.159A 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: 5.855A 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: 5.855A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 249 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 122 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 123 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 147 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.986A 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 46 removed outlier: 6.927A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.558A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.266A 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: 5.855A 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: 5.855A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 249 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 122 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 46 removed outlier: 7.037A 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 46 removed outlier: 5.588A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 261 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.229A 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: 5.814A 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: 5.814A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 249 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY E 122 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 123 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 3.978A 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 46 removed outlier: 7.030A 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 46 removed outlier: 5.547A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.145A 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: 5.771A 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: 5.771A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 249 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY F 122 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1836 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: 4.34 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4624 1.34 - 1.46: 2940 1.46 - 1.58: 6166 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" N LEU H 72 " pdb=" CA LEU H 72 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.68e+00 bond pdb=" N LEU D 72 " pdb=" CA LEU D 72 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.52e+00 bond pdb=" N VAL A 58 " pdb=" CA VAL A 58 " ideal model delta sigma weight residual 1.459 1.446 0.013 1.25e-02 6.40e+03 1.04e+00 bond pdb=" CA LEU H 72 " pdb=" C LEU H 72 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.35e-02 5.49e+03 6.87e-01 bond pdb=" CB PHE A 52 " pdb=" CG PHE A 52 " ideal model delta sigma weight residual 1.502 1.521 -0.019 2.30e-02 1.89e+03 6.82e-01 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 18328 1.68 - 3.36: 278 3.36 - 5.04: 19 5.04 - 6.72: 3 6.72 - 8.40: 2 Bond angle restraints: 18630 Sorted by residual: angle pdb=" N LEU D 72 " pdb=" CA LEU D 72 " pdb=" C LEU D 72 " ideal model delta sigma weight residual 111.28 108.52 2.76 1.09e+00 8.42e-01 6.39e+00 angle pdb=" CA LEU D 72 " pdb=" C LEU D 72 " pdb=" O LEU D 72 " ideal model delta sigma weight residual 120.55 117.94 2.61 1.06e+00 8.90e-01 6.07e+00 angle pdb=" CA LEU G 117 " pdb=" CB LEU G 117 " pdb=" CG LEU G 117 " ideal model delta sigma weight residual 116.30 124.70 -8.40 3.50e+00 8.16e-02 5.76e+00 angle pdb=" CA LEU C 117 " pdb=" CB LEU C 117 " pdb=" CG LEU C 117 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.63e+00 angle pdb=" CA GLN B 173 " pdb=" CB GLN B 173 " pdb=" CG GLN B 173 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.67e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 7033 15.26 - 30.52: 847 30.52 - 45.78: 238 45.78 - 61.03: 80 61.03 - 76.29: 50 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA TRP B 126 " pdb=" C TRP B 126 " pdb=" N TYR B 127 " pdb=" CA TYR B 127 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+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 -118.21 32.21 1 1.00e+01 1.00e-02 1.48e+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 -117.56 31.56 1 1.00e+01 1.00e-02 1.42e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1059 0.029 - 0.059: 547 0.059 - 0.088: 172 0.088 - 0.117: 107 0.117 - 0.147: 31 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA VAL F 93 " pdb=" N VAL F 93 " pdb=" C VAL F 93 " pdb=" CB VAL F 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 238 " pdb=" N ILE B 238 " pdb=" C ILE B 238 " pdb=" CB ILE B 238 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 54 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 55 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 128 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ALA A 128 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA A 128 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 129 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 68 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO H 69 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 69 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 69 " -0.018 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 37 2.31 - 2.96: 5957 2.96 - 3.61: 19536 3.61 - 4.25: 31040 4.25 - 4.90: 52691 Nonbonded interactions: 109261 Sorted by model distance: nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.666 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.714 3.040 nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 162 " model vdw 1.732 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 162 " model vdw 1.741 3.040 nonbonded pdb=" NE2 HIS G 99 " pdb="ZN ZN G 703 " model vdw 1.995 2.310 ... (remaining 109256 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: 0.710 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.770 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.003 0.029 13794 Z= 0.205 Angle : 0.507 8.403 18630 Z= 0.280 Chirality : 0.044 0.147 1916 Planarity : 0.004 0.037 2510 Dihedral : 16.109 76.292 5140 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 10.65 % Favored : 89.21 % 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: -0.23 (0.20), residues: 1650 helix: 1.18 (0.23), residues: 490 sheet: 0.17 (0.28), residues: 362 loop : -1.17 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 126 HIS 0.006 0.001 HIS C 51 PHE 0.015 0.001 PHE B 52 TYR 0.013 0.001 TYR H 76 ARG 0.005 0.001 ARG F 45 *********************** 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 341 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 1.426 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: A 159 LYS cc_start: 0.8479 (mptt) cc_final: 0.7395 (tptt) REVERT: A 297 GLN cc_start: 0.9044 (mt0) cc_final: 0.8252 (mt0) REVERT: B 295 HIS cc_start: 0.8988 (t70) cc_final: 0.8784 (t70) REVERT: B 340 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7669 (mtp85) REVERT: C 48 ASP cc_start: 0.8511 (t0) cc_final: 0.8034 (t0) REVERT: C 132 ASN cc_start: 0.9064 (t0) cc_final: 0.8694 (t0) REVERT: D 45 THR cc_start: 0.9372 (p) cc_final: 0.8976 (p) REVERT: D 72 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8577 (pp) REVERT: D 89 ASP cc_start: 0.8350 (p0) cc_final: 0.7988 (p0) REVERT: D 115 ASP cc_start: 0.8289 (m-30) cc_final: 0.7304 (m-30) REVERT: D 127 ASP cc_start: 0.8473 (m-30) cc_final: 0.8159 (m-30) REVERT: E 48 TYR cc_start: 0.8530 (p90) cc_final: 0.8316 (p90) REVERT: E 85 SER cc_start: 0.8828 (t) cc_final: 0.8496 (t) REVERT: E 118 ILE cc_start: 0.8402 (mm) cc_final: 0.7855 (mm) REVERT: E 137 VAL cc_start: 0.7941 (t) cc_final: 0.7538 (p) REVERT: E 207 TYR cc_start: 0.7641 (t80) cc_final: 0.7378 (t80) REVERT: E 330 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7243 (pt0) REVERT: E 351 GLN cc_start: 0.7902 (tt0) cc_final: 0.7639 (tm-30) REVERT: F 215 MET cc_start: 0.8741 (mtp) cc_final: 0.8383 (mtm) REVERT: G 48 ASP cc_start: 0.8729 (t0) cc_final: 0.8202 (m-30) REVERT: G 138 TYR cc_start: 0.8572 (t80) cc_final: 0.8227 (t80) REVERT: H 53 MET cc_start: 0.9149 (mmm) cc_final: 0.8905 (mmt) REVERT: H 75 HIS cc_start: 0.8561 (m-70) cc_final: 0.8249 (m-70) REVERT: H 77 PHE cc_start: 0.8262 (t80) cc_final: 0.8044 (t80) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.3018 time to fit residues: 142.1883 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 351 GLN B 175 HIS B 178 HIS B 191 GLN B 241 GLN B 333 GLN B 342 HIS C 49 GLN C 73 GLN C 80 HIS D 70 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS E 298 GLN E 351 GLN F 191 GLN F 241 GLN F 333 GLN G 70 GLN G 80 HIS H 70 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13794 Z= 0.395 Angle : 0.617 9.204 18630 Z= 0.328 Chirality : 0.047 0.156 1916 Planarity : 0.004 0.044 2510 Dihedral : 4.415 26.033 1790 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.25 % Allowed : 12.93 % Favored : 83.82 % 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: -0.26 (0.20), residues: 1650 helix: 1.44 (0.23), residues: 500 sheet: -0.17 (0.28), residues: 352 loop : -1.23 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 126 HIS 0.017 0.001 HIS H 80 PHE 0.027 0.002 PHE B 52 TYR 0.031 0.002 TYR B 208 ARG 0.007 0.001 ARG B 117 *********************** 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 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 1.720 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: A 159 LYS cc_start: 0.8642 (mptt) cc_final: 0.7560 (tptt) REVERT: A 192 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (mmt-90) REVERT: A 297 GLN cc_start: 0.8872 (mt0) cc_final: 0.8584 (mt0) REVERT: B 289 TYR cc_start: 0.8964 (m-80) cc_final: 0.8740 (m-10) REVERT: B 340 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7704 (mtp85) REVERT: B 354 MET cc_start: 0.8716 (tmm) cc_final: 0.8397 (tmm) REVERT: B 355 ILE cc_start: 0.7634 (tt) cc_final: 0.7411 (tt) REVERT: C 75 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8353 (t-90) REVERT: C 132 ASN cc_start: 0.9127 (t0) cc_final: 0.8775 (t0) REVERT: D 129 ASP cc_start: 0.7381 (t0) cc_final: 0.6843 (t0) REVERT: D 131 ASN cc_start: 0.8205 (p0) cc_final: 0.7980 (p0) REVERT: E 48 TYR cc_start: 0.8704 (p90) cc_final: 0.8467 (p90) REVERT: E 118 ILE cc_start: 0.8418 (mm) cc_final: 0.8062 (mm) REVERT: G 48 ASP cc_start: 0.8785 (t0) cc_final: 0.8326 (m-30) REVERT: G 49 GLN cc_start: 0.9007 (pp30) cc_final: 0.8727 (pp30) REVERT: G 52 ILE cc_start: 0.9394 (tp) cc_final: 0.8994 (tp) REVERT: G 73 GLN cc_start: 0.8391 (pp30) cc_final: 0.8152 (pp30) REVERT: G 140 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7489 (tt0) REVERT: H 75 HIS cc_start: 0.8616 (m-70) cc_final: 0.8273 (m-70) REVERT: H 117 LEU cc_start: 0.8381 (tp) cc_final: 0.8155 (tp) REVERT: H 132 ASN cc_start: 0.7467 (t0) cc_final: 0.7097 (t0) outliers start: 47 outliers final: 25 residues processed: 283 average time/residue: 0.2862 time to fit residues: 114.3057 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 101 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: 1.9990 chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 191 GLN B 196 ASN B 298 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS F 191 GLN G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13794 Z= 0.298 Angle : 0.574 7.593 18630 Z= 0.304 Chirality : 0.046 0.163 1916 Planarity : 0.004 0.076 2510 Dihedral : 4.376 22.901 1788 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.18 % Allowed : 15.49 % Favored : 81.33 % 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: -0.32 (0.20), residues: 1650 helix: 1.39 (0.24), residues: 502 sheet: -0.10 (0.29), residues: 338 loop : -1.31 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 126 HIS 0.010 0.001 HIS H 80 PHE 0.028 0.002 PHE H 77 TYR 0.026 0.002 TYR B 208 ARG 0.008 0.001 ARG C 126 *********************** 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 285 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 1.466 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: A 159 LYS cc_start: 0.8613 (mptt) cc_final: 0.7545 (tptt) REVERT: A 192 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (mmt-90) REVERT: A 297 GLN cc_start: 0.8867 (mt0) cc_final: 0.8404 (mt0) REVERT: A 350 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7617 (mtm-85) REVERT: B 207 TYR cc_start: 0.9191 (t80) cc_final: 0.8612 (t80) REVERT: B 340 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7712 (mtp85) REVERT: B 354 MET cc_start: 0.8732 (tmm) cc_final: 0.8338 (tmm) REVERT: C 48 ASP cc_start: 0.8088 (t0) cc_final: 0.7725 (t70) REVERT: C 53 MET cc_start: 0.8972 (mmm) cc_final: 0.8631 (mmm) REVERT: C 75 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8324 (t-90) REVERT: C 132 ASN cc_start: 0.9133 (t0) cc_final: 0.8783 (t0) REVERT: D 53 MET cc_start: 0.8940 (mmm) cc_final: 0.8640 (mmm) REVERT: D 67 MET cc_start: 0.8344 (mmp) cc_final: 0.7572 (ttm) REVERT: D 129 ASP cc_start: 0.7524 (t0) cc_final: 0.6958 (t0) REVERT: D 131 ASN cc_start: 0.8267 (p0) cc_final: 0.7995 (p0) REVERT: E 118 ILE cc_start: 0.8513 (mm) cc_final: 0.8239 (mm) REVERT: G 48 ASP cc_start: 0.8791 (t0) cc_final: 0.8321 (m-30) REVERT: G 49 GLN cc_start: 0.8898 (pp30) cc_final: 0.8587 (pp30) REVERT: G 71 GLU cc_start: 0.8947 (tt0) cc_final: 0.8348 (tm-30) REVERT: G 73 GLN cc_start: 0.8491 (pp30) cc_final: 0.8235 (pp30) REVERT: G 140 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7308 (tt0) REVERT: H 75 HIS cc_start: 0.8615 (m-70) cc_final: 0.8293 (m-70) REVERT: H 86 ASN cc_start: 0.8834 (t0) cc_final: 0.7939 (t0) REVERT: H 132 ASN cc_start: 0.7567 (t0) cc_final: 0.7014 (t0) outliers start: 46 outliers final: 28 residues processed: 265 average time/residue: 0.2815 time to fit residues: 105.6233 Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 191 GLN Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS B 191 GLN C 49 GLN C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS F 79 GLN G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13794 Z= 0.284 Angle : 0.570 8.702 18630 Z= 0.302 Chirality : 0.045 0.148 1916 Planarity : 0.004 0.061 2510 Dihedral : 4.339 23.130 1788 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.18 % Allowed : 16.18 % Favored : 80.64 % 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: -0.33 (0.20), residues: 1650 helix: 1.35 (0.23), residues: 502 sheet: -0.07 (0.30), residues: 310 loop : -1.28 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 126 HIS 0.011 0.001 HIS H 80 PHE 0.027 0.002 PHE H 77 TYR 0.023 0.002 TYR B 208 ARG 0.007 0.001 ARG F 350 *********************** 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 280 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.581 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 159 LYS cc_start: 0.8589 (mptt) cc_final: 0.7541 (tptt) REVERT: A 192 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8731 (mmt-90) REVERT: A 226 ASP cc_start: 0.8430 (t70) cc_final: 0.7604 (t0) REVERT: A 297 GLN cc_start: 0.8858 (mt0) cc_final: 0.8502 (mt0) REVERT: B 207 TYR cc_start: 0.9212 (t80) cc_final: 0.8623 (t80) REVERT: B 340 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7684 (mtp85) REVERT: C 48 ASP cc_start: 0.8081 (t0) cc_final: 0.7774 (t70) REVERT: C 57 GLU cc_start: 0.9021 (tt0) cc_final: 0.8815 (tm-30) REVERT: C 75 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: C 132 ASN cc_start: 0.9141 (t0) cc_final: 0.8799 (t0) REVERT: D 53 MET cc_start: 0.9002 (mmm) cc_final: 0.8628 (mmm) REVERT: D 67 MET cc_start: 0.8339 (mmp) cc_final: 0.7318 (ttm) REVERT: D 112 MET cc_start: 0.8773 (tmm) cc_final: 0.8558 (tmm) REVERT: D 119 ASN cc_start: 0.8777 (p0) cc_final: 0.8470 (p0) REVERT: D 129 ASP cc_start: 0.7613 (t0) cc_final: 0.7117 (t70) REVERT: D 131 ASN cc_start: 0.8356 (p0) cc_final: 0.8110 (p0) REVERT: E 118 ILE cc_start: 0.8490 (mm) cc_final: 0.8275 (mm) REVERT: E 207 TYR cc_start: 0.8031 (t80) cc_final: 0.7682 (t80) REVERT: G 47 HIS cc_start: 0.9214 (m-70) cc_final: 0.8861 (m-70) REVERT: G 71 GLU cc_start: 0.8944 (tt0) cc_final: 0.8437 (tm-30) REVERT: G 73 GLN cc_start: 0.8554 (pp30) cc_final: 0.8290 (pp30) REVERT: H 75 HIS cc_start: 0.8599 (m-70) cc_final: 0.8279 (m-70) REVERT: H 86 ASN cc_start: 0.8882 (t0) cc_final: 0.8139 (t0) REVERT: H 132 ASN cc_start: 0.7703 (t0) cc_final: 0.7168 (t0) outliers start: 46 outliers final: 32 residues processed: 264 average time/residue: 0.2846 time to fit residues: 106.7483 Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE 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 86 ASN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN F 359 GLN G 70 GLN G 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13794 Z= 0.425 Angle : 0.621 8.696 18630 Z= 0.329 Chirality : 0.048 0.157 1916 Planarity : 0.004 0.061 2510 Dihedral : 4.552 23.912 1788 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.60 % Allowed : 16.46 % Favored : 79.94 % 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: -0.47 (0.20), residues: 1650 helix: 1.19 (0.23), residues: 500 sheet: -0.17 (0.31), residues: 314 loop : -1.33 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 126 HIS 0.010 0.001 HIS H 80 PHE 0.026 0.002 PHE B 52 TYR 0.024 0.002 TYR B 208 ARG 0.009 0.001 ARG B 117 *********************** 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 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 1.619 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 159 LYS cc_start: 0.8617 (mptt) cc_final: 0.7578 (tptt) REVERT: A 350 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7654 (mtm-85) REVERT: B 340 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: C 48 ASP cc_start: 0.8133 (t0) cc_final: 0.7831 (t70) REVERT: C 57 GLU cc_start: 0.9057 (tt0) cc_final: 0.8844 (tm-30) REVERT: C 75 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8314 (t-90) REVERT: C 126 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8456 (ttp80) REVERT: C 132 ASN cc_start: 0.9152 (t0) cc_final: 0.8849 (t0) REVERT: D 53 MET cc_start: 0.9016 (mmm) cc_final: 0.8673 (mmm) REVERT: D 112 MET cc_start: 0.8776 (tmm) cc_final: 0.8420 (tmm) REVERT: D 119 ASN cc_start: 0.8678 (p0) cc_final: 0.8452 (p0) REVERT: D 127 ASP cc_start: 0.8493 (m-30) cc_final: 0.8240 (m-30) REVERT: E 192 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8042 (mmt180) REVERT: E 207 TYR cc_start: 0.8099 (t80) cc_final: 0.7748 (t80) REVERT: E 352 LEU cc_start: 0.8173 (tp) cc_final: 0.7732 (tt) REVERT: G 47 HIS cc_start: 0.9247 (m-70) cc_final: 0.8906 (m-70) REVERT: G 71 GLU cc_start: 0.8963 (tt0) cc_final: 0.8433 (tm-30) REVERT: G 73 GLN cc_start: 0.8559 (pp30) cc_final: 0.8293 (pp30) REVERT: G 112 MET cc_start: 0.8526 (tmm) cc_final: 0.8167 (tmm) REVERT: G 116 GLU cc_start: 0.7727 (mp0) cc_final: 0.7526 (mp0) REVERT: H 75 HIS cc_start: 0.8596 (m-70) cc_final: 0.8285 (m-70) REVERT: H 86 ASN cc_start: 0.8963 (t0) cc_final: 0.8095 (t0) REVERT: H 132 ASN cc_start: 0.7889 (t0) cc_final: 0.7354 (t0) outliers start: 52 outliers final: 38 residues processed: 258 average time/residue: 0.2852 time to fit residues: 103.7361 Evaluate side-chains 252 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13794 Z= 0.236 Angle : 0.579 9.678 18630 Z= 0.306 Chirality : 0.045 0.145 1916 Planarity : 0.004 0.051 2510 Dihedral : 4.399 23.330 1788 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.32 % Allowed : 17.63 % Favored : 79.05 % 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: -0.37 (0.20), residues: 1650 helix: 1.18 (0.23), residues: 504 sheet: 0.07 (0.32), residues: 300 loop : -1.27 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.008 0.001 HIS H 80 PHE 0.022 0.002 PHE H 77 TYR 0.025 0.002 TYR G 138 ARG 0.012 0.001 ARG B 117 *********************** 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: 48 poor density : 243 time to evaluate : 1.515 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 159 LYS cc_start: 0.8590 (mptt) cc_final: 0.7618 (tptt) REVERT: B 207 TYR cc_start: 0.9224 (t80) cc_final: 0.8777 (t80) REVERT: B 340 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7641 (mtp85) REVERT: C 57 GLU cc_start: 0.9020 (tt0) cc_final: 0.8811 (tm-30) REVERT: C 75 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8267 (t-90) REVERT: C 132 ASN cc_start: 0.9157 (t0) cc_final: 0.8897 (t0) REVERT: D 53 MET cc_start: 0.9011 (mmm) cc_final: 0.8678 (mmp) REVERT: D 112 MET cc_start: 0.8715 (tmm) cc_final: 0.8401 (tmm) REVERT: D 127 ASP cc_start: 0.8492 (m-30) cc_final: 0.8266 (m-30) REVERT: E 137 VAL cc_start: 0.8272 (t) cc_final: 0.8028 (p) REVERT: E 207 TYR cc_start: 0.8073 (t80) cc_final: 0.7765 (t80) REVERT: E 232 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8383 (ttpt) REVERT: E 352 LEU cc_start: 0.8187 (tp) cc_final: 0.7663 (tt) REVERT: G 47 HIS cc_start: 0.9221 (m-70) cc_final: 0.8876 (m-70) REVERT: G 71 GLU cc_start: 0.8965 (tt0) cc_final: 0.8491 (tm-30) REVERT: G 73 GLN cc_start: 0.8513 (pp30) cc_final: 0.8242 (pp30) REVERT: G 138 TYR cc_start: 0.8877 (t80) cc_final: 0.8585 (t80) REVERT: H 75 HIS cc_start: 0.8587 (m-70) cc_final: 0.8202 (m-70) REVERT: H 86 ASN cc_start: 0.8928 (t0) cc_final: 0.8091 (t0) REVERT: H 132 ASN cc_start: 0.7827 (t0) cc_final: 0.7307 (t0) outliers start: 48 outliers final: 35 residues processed: 274 average time/residue: 0.2838 time to fit residues: 110.3917 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 135 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13794 Z= 0.331 Angle : 0.624 10.175 18630 Z= 0.329 Chirality : 0.047 0.207 1916 Planarity : 0.004 0.052 2510 Dihedral : 4.454 24.032 1788 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.11 % Allowed : 19.43 % Favored : 77.46 % 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: -0.38 (0.20), residues: 1650 helix: 1.12 (0.23), residues: 502 sheet: -0.07 (0.30), residues: 336 loop : -1.22 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 126 HIS 0.009 0.001 HIS H 80 PHE 0.022 0.002 PHE B 52 TYR 0.023 0.002 TYR C 138 ARG 0.009 0.001 ARG C 126 *********************** 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 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 1.504 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: A 159 LYS cc_start: 0.8601 (mptt) cc_final: 0.7605 (tptt) REVERT: B 340 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7639 (mtp85) REVERT: C 75 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8196 (t-90) REVERT: C 126 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8395 (ttp80) REVERT: C 132 ASN cc_start: 0.9162 (t0) cc_final: 0.8921 (t0) REVERT: D 53 MET cc_start: 0.9054 (mmm) cc_final: 0.8738 (mmp) REVERT: D 70 GLN cc_start: 0.8888 (pm20) cc_final: 0.8687 (pm20) REVERT: D 112 MET cc_start: 0.8700 (tmm) cc_final: 0.8384 (tmm) REVERT: D 127 ASP cc_start: 0.8482 (m-30) cc_final: 0.8264 (m-30) REVERT: E 207 TYR cc_start: 0.8098 (t80) cc_final: 0.7763 (t80) REVERT: E 352 LEU cc_start: 0.8224 (tp) cc_final: 0.7692 (tt) REVERT: G 47 HIS cc_start: 0.9250 (m-70) cc_final: 0.8910 (m-70) REVERT: G 71 GLU cc_start: 0.8907 (tt0) cc_final: 0.8545 (tm-30) REVERT: G 73 GLN cc_start: 0.8499 (pp30) cc_final: 0.8253 (pp30) REVERT: G 112 MET cc_start: 0.8606 (tmm) cc_final: 0.8305 (tmm) REVERT: H 75 HIS cc_start: 0.8571 (m-70) cc_final: 0.8231 (m-70) REVERT: H 86 ASN cc_start: 0.8945 (t0) cc_final: 0.8371 (t0) REVERT: H 132 ASN cc_start: 0.7856 (t0) cc_final: 0.7337 (t0) outliers start: 45 outliers final: 38 residues processed: 253 average time/residue: 0.2905 time to fit residues: 104.1785 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13794 Z= 0.186 Angle : 0.593 10.543 18630 Z= 0.311 Chirality : 0.045 0.189 1916 Planarity : 0.003 0.044 2510 Dihedral : 4.291 24.057 1788 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.90 % Allowed : 19.85 % Favored : 77.25 % 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 (0.20), residues: 1650 helix: 1.13 (0.24), residues: 504 sheet: 0.15 (0.30), residues: 334 loop : -1.10 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 126 HIS 0.013 0.001 HIS D 99 PHE 0.018 0.001 PHE H 77 TYR 0.022 0.001 TYR C 76 ARG 0.009 0.001 ARG H 126 *********************** 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 273 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 1.324 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: A 159 LYS cc_start: 0.8585 (mptt) cc_final: 0.7587 (tptt) REVERT: B 207 TYR cc_start: 0.9206 (t80) cc_final: 0.8697 (t80) REVERT: B 215 MET cc_start: 0.8939 (mtp) cc_final: 0.8655 (mtp) REVERT: B 340 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7641 (mtp85) REVERT: B 354 MET cc_start: 0.8765 (tmm) cc_final: 0.8208 (tmm) REVERT: C 75 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8221 (t-90) REVERT: C 132 ASN cc_start: 0.9154 (t0) cc_final: 0.8884 (t0) REVERT: D 53 MET cc_start: 0.9023 (mmm) cc_final: 0.8712 (mmp) REVERT: D 112 MET cc_start: 0.8659 (tmm) cc_final: 0.8352 (tmm) REVERT: D 115 ASP cc_start: 0.8061 (m-30) cc_final: 0.7801 (m-30) REVERT: E 207 TYR cc_start: 0.8024 (t80) cc_final: 0.7721 (t80) REVERT: E 352 LEU cc_start: 0.8210 (tp) cc_final: 0.7661 (tt) REVERT: G 47 HIS cc_start: 0.9243 (m-70) cc_final: 0.8909 (m-70) REVERT: G 67 MET cc_start: 0.7576 (mmm) cc_final: 0.7371 (mmm) REVERT: G 70 GLN cc_start: 0.8505 (pm20) cc_final: 0.8255 (pm20) REVERT: G 71 GLU cc_start: 0.8935 (tt0) cc_final: 0.8436 (tm-30) REVERT: G 73 GLN cc_start: 0.8496 (pp30) cc_final: 0.8272 (pp30) REVERT: G 112 MET cc_start: 0.8591 (tmm) cc_final: 0.8299 (tmm) REVERT: G 132 ASN cc_start: 0.8824 (t0) cc_final: 0.7904 (t0) REVERT: H 75 HIS cc_start: 0.8547 (m-70) cc_final: 0.8184 (m-70) REVERT: H 77 PHE cc_start: 0.8042 (t80) cc_final: 0.7794 (t80) REVERT: H 132 ASN cc_start: 0.7813 (t0) cc_final: 0.7279 (t0) outliers start: 42 outliers final: 34 residues processed: 258 average time/residue: 0.2887 time to fit residues: 106.5778 Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13794 Z= 0.235 Angle : 0.633 17.069 18630 Z= 0.330 Chirality : 0.046 0.226 1916 Planarity : 0.004 0.059 2510 Dihedral : 4.334 23.967 1788 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.56 % Allowed : 20.61 % Favored : 76.83 % 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: -0.24 (0.20), residues: 1650 helix: 1.04 (0.24), residues: 504 sheet: 0.07 (0.29), residues: 344 loop : -1.03 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.011 0.001 HIS D 99 PHE 0.022 0.002 PHE E 296 TYR 0.028 0.002 TYR C 138 ARG 0.011 0.001 ARG G 126 *********************** 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 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.448 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: A 159 LYS cc_start: 0.8569 (mptt) cc_final: 0.7568 (tptt) REVERT: B 207 TYR cc_start: 0.9260 (t80) cc_final: 0.8742 (t80) REVERT: B 215 MET cc_start: 0.8941 (mtp) cc_final: 0.8686 (mtp) REVERT: B 340 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7629 (mtp85) REVERT: B 354 MET cc_start: 0.8799 (tmm) cc_final: 0.8228 (tmm) REVERT: C 132 ASN cc_start: 0.9158 (t0) cc_final: 0.8896 (t0) REVERT: D 53 MET cc_start: 0.9030 (mmm) cc_final: 0.8727 (mmp) REVERT: D 70 GLN cc_start: 0.8885 (pm20) cc_final: 0.8620 (pm20) REVERT: D 112 MET cc_start: 0.8674 (tmm) cc_final: 0.8276 (tmm) REVERT: D 115 ASP cc_start: 0.8120 (m-30) cc_final: 0.7813 (m-30) REVERT: E 199 TYR cc_start: 0.8333 (m-80) cc_final: 0.8084 (m-10) REVERT: E 207 TYR cc_start: 0.8034 (t80) cc_final: 0.7682 (t80) REVERT: E 352 LEU cc_start: 0.8198 (tp) cc_final: 0.7657 (tt) REVERT: G 47 HIS cc_start: 0.9240 (m-70) cc_final: 0.8848 (m-70) REVERT: G 70 GLN cc_start: 0.8391 (pm20) cc_final: 0.8068 (pm20) REVERT: G 71 GLU cc_start: 0.8922 (tt0) cc_final: 0.8425 (tm-30) REVERT: G 73 GLN cc_start: 0.8460 (pp30) cc_final: 0.8218 (pp30) REVERT: G 112 MET cc_start: 0.8607 (tmm) cc_final: 0.8302 (tmm) REVERT: G 132 ASN cc_start: 0.8845 (t0) cc_final: 0.7945 (t0) REVERT: H 77 PHE cc_start: 0.8065 (t80) cc_final: 0.7793 (t80) REVERT: H 86 ASN cc_start: 0.8888 (t0) cc_final: 0.8352 (t0) REVERT: H 132 ASN cc_start: 0.7767 (t0) cc_final: 0.7309 (t0) outliers start: 37 outliers final: 33 residues processed: 246 average time/residue: 0.2760 time to fit residues: 96.6900 Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13794 Z= 0.237 Angle : 0.648 15.703 18630 Z= 0.337 Chirality : 0.046 0.200 1916 Planarity : 0.004 0.053 2510 Dihedral : 4.333 23.421 1788 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.63 % Allowed : 20.47 % 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: -0.29 (0.20), residues: 1650 helix: 0.98 (0.23), residues: 504 sheet: 0.05 (0.29), residues: 346 loop : -1.05 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.010 0.001 HIS D 99 PHE 0.072 0.002 PHE E 296 TYR 0.039 0.002 TYR B 289 ARG 0.013 0.001 ARG H 126 ********************** 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 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.491 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: A 159 LYS cc_start: 0.8571 (mptt) cc_final: 0.7578 (tptt) REVERT: B 207 TYR cc_start: 0.9257 (t80) cc_final: 0.8793 (t80) REVERT: B 215 MET cc_start: 0.8940 (mtp) cc_final: 0.8679 (mtp) REVERT: B 340 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7630 (mtp85) REVERT: B 354 MET cc_start: 0.8813 (tmm) cc_final: 0.8275 (tmm) REVERT: C 86 ASN cc_start: 0.8456 (m110) cc_final: 0.8254 (t0) REVERT: C 132 ASN cc_start: 0.9160 (t0) cc_final: 0.8907 (t0) REVERT: D 53 MET cc_start: 0.9026 (mmm) cc_final: 0.8732 (mmp) REVERT: D 70 GLN cc_start: 0.8904 (pm20) cc_final: 0.8662 (pm20) REVERT: D 112 MET cc_start: 0.8648 (tmm) cc_final: 0.8224 (tmm) REVERT: D 115 ASP cc_start: 0.8148 (m-30) cc_final: 0.7876 (m-30) REVERT: E 199 TYR cc_start: 0.8350 (m-80) cc_final: 0.8075 (m-10) REVERT: E 207 TYR cc_start: 0.8056 (t80) cc_final: 0.7706 (t80) REVERT: E 352 LEU cc_start: 0.8195 (tp) cc_final: 0.7644 (tt) REVERT: G 47 HIS cc_start: 0.9234 (m-70) cc_final: 0.8861 (m-70) REVERT: G 70 GLN cc_start: 0.8330 (pm20) cc_final: 0.8048 (pm20) REVERT: G 73 GLN cc_start: 0.8435 (pp30) cc_final: 0.8205 (pp30) REVERT: G 112 MET cc_start: 0.8635 (tmm) cc_final: 0.8320 (tmm) REVERT: G 132 ASN cc_start: 0.8842 (t0) cc_final: 0.7943 (t0) REVERT: G 140 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6002 (mt-10) REVERT: H 75 HIS cc_start: 0.8509 (m-70) cc_final: 0.8130 (m-70) REVERT: H 77 PHE cc_start: 0.8011 (t80) cc_final: 0.7756 (t80) REVERT: H 85 ASN cc_start: 0.8785 (p0) cc_final: 0.8412 (p0) REVERT: H 86 ASN cc_start: 0.8949 (t0) cc_final: 0.8265 (t0) REVERT: H 132 ASN cc_start: 0.7927 (t0) cc_final: 0.7322 (t0) outliers start: 38 outliers final: 35 residues processed: 247 average time/residue: 0.2659 time to fit residues: 94.2791 Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098558 restraints weight = 19913.947| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.20 r_work: 0.2966 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13794 Z= 0.200 Angle : 0.654 16.067 18630 Z= 0.340 Chirality : 0.046 0.196 1916 Planarity : 0.004 0.086 2510 Dihedral : 4.292 23.121 1788 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 21.02 % Favored : 76.56 % 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: -0.15 (0.20), residues: 1650 helix: 1.12 (0.24), residues: 490 sheet: 0.20 (0.29), residues: 336 loop : -0.97 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.010 0.001 HIS D 99 PHE 0.065 0.002 PHE E 296 TYR 0.031 0.002 TYR B 289 ARG 0.012 0.001 ARG H 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.14 seconds wall clock time: 57 minutes 0.85 seconds (3420.85 seconds total)