Starting phenix.real_space_refine on Fri Jul 3 09:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2026/8jp7_36470.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.116 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 38 5.16 5 C 8452 2.51 5 N 2340 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13476 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2612 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 307} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "E" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2612 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 307} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "H" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.30, per 1000 atoms: 0.24 Number of scatterers: 13476 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 38 16.00 O 2626 8.00 N 2340 7.00 C 8452 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: 1.07 Conformation dependent library (CDL) restraints added in 663.6 milliseconds 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 16 sheets defined 33.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.550A pdb=" N SER A 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 283 through 308 removed outlier: 3.620A pdb=" N GLU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 325 through 365 removed outlier: 3.823A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.578A pdb=" N ASN B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 284 through 308 removed outlier: 4.392A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 365 removed outlier: 3.662A pdb=" N SER B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.579A pdb=" N SER C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 removed outlier: 3.609A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 4.583A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.604A pdb=" N GLN D 73 " --> pdb=" O PRO D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.714A pdb=" N ASP D 127 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.501A pdb=" N SER E 51 " --> pdb=" O TYR E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 283 through 308 removed outlier: 3.625A pdb=" N GLU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 325 through 365 removed outlier: 3.801A pdb=" N VAL E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 365 " --> pdb=" O ARG E 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 89 through 99 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 144 removed outlier: 3.567A pdb=" N SER G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 47 removed outlier: 3.633A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 removed outlier: 4.477A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 57 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 removed outlier: 3.610A pdb=" N GLN H 73 " --> pdb=" O PRO H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.566A pdb=" N ASP H 127 " --> pdb=" O GLY H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.681A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.696A 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 280 through 283 Processing helix chain 'F' and resid 284 through 308 removed outlier: 4.400A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 365 removed outlier: 4.024A pdb=" N SER F 365 " --> pdb=" O ARG F 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.954A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 5.602A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 261 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 103 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 202 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.146A 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: 5.804A 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: 5.804A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.660A 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 52 removed outlier: 11.127A pdb=" N PHE B 46 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N THR B 268 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TYR B 48 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLN B 266 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 50 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 264 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 52 removed outlier: 11.127A pdb=" N PHE B 46 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N THR B 268 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TYR B 48 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLN B 266 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 50 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 264 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 261 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.147A 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: 3.505A pdb=" N GLN B 89 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.795A 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: 3.505A pdb=" N GLN B 89 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.813A 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: 6.865A 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: 5.619A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 261 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 202 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.066A 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: 5.758A 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: 5.758A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.695A 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 52 removed outlier: 4.582A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.897A 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 52 removed outlier: 4.582A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F 261 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.198A 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: 5.845A 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: 5.845A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.46 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: 4616 1.34 - 1.47: 3129 1.47 - 1.59: 5957 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 13770 Sorted by residual: bond pdb=" N LEU C 74 " pdb=" CA LEU C 74 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.29e+00 bond pdb=" N LEU D 111 " pdb=" CA LEU D 111 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.25e-02 6.40e+03 4.76e+00 bond pdb=" N PHE E 296 " pdb=" CA PHE E 296 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.40e+00 bond pdb=" N LEU G 74 " pdb=" CA LEU G 74 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.83e+00 bond pdb=" CG LEU D 74 " pdb=" CD1 LEU D 74 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 ... (remaining 13765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18253 1.99 - 3.97: 299 3.97 - 5.96: 33 5.96 - 7.94: 9 7.94 - 9.93: 4 Bond angle restraints: 18598 Sorted by residual: angle pdb=" C ALA E 120 " pdb=" N ASP E 121 " pdb=" CA ASP E 121 " ideal model delta sigma weight residual 121.70 129.44 -7.74 1.80e+00 3.09e-01 1.85e+01 angle pdb=" C ALA A 120 " pdb=" N ASP A 121 " pdb=" CA ASP A 121 " ideal model delta sigma weight residual 121.70 129.43 -7.73 1.80e+00 3.09e-01 1.84e+01 angle pdb=" C ALA B 120 " pdb=" N ASP B 121 " pdb=" CA ASP B 121 " ideal model delta sigma weight residual 121.70 128.63 -6.93 1.80e+00 3.09e-01 1.48e+01 angle pdb=" C ALA F 120 " pdb=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.93e+00 angle pdb=" CA ILE H 52 " pdb=" CB ILE H 52 " pdb=" CG1 ILE H 52 " ideal model delta sigma weight residual 110.40 115.54 -5.14 1.70e+00 3.46e-01 9.15e+00 ... (remaining 18593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7004 17.46 - 34.92: 894 34.92 - 52.38: 252 52.38 - 69.84: 68 69.84 - 87.30: 18 Dihedral angle restraints: 8236 sinusoidal: 3428 harmonic: 4808 Sorted by residual: dihedral pdb=" CA THR C 98 " pdb=" C THR C 98 " pdb=" N HIS C 99 " pdb=" CA HIS C 99 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR G 98 " pdb=" C THR G 98 " pdb=" N HIS G 99 " pdb=" CA HIS G 99 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP F 126 " pdb=" C TRP F 126 " pdb=" N TYR F 127 " pdb=" CA TYR F 127 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1387 0.049 - 0.099: 398 0.099 - 0.148: 117 0.148 - 0.197: 8 0.197 - 0.246: 2 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CG LEU D 56 " pdb=" CB LEU D 56 " pdb=" CD1 LEU D 56 " pdb=" CD2 LEU D 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE D 60 " pdb=" CA ILE D 60 " pdb=" CG1 ILE D 60 " pdb=" CG2 ILE D 60 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA LEU C 74 " pdb=" N LEU C 74 " pdb=" C LEU C 74 " pdb=" CB LEU C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 1909 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 99 " 0.017 2.00e-02 2.50e+03 2.25e-02 7.58e+00 pdb=" CG HIS H 99 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS H 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS H 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS H 99 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS H 99 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 99 " -0.018 2.00e-02 2.50e+03 1.50e-02 3.39e+00 pdb=" CG HIS D 99 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS D 99 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS D 99 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS D 99 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ASN D 61 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN D 61 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS D 62 " 0.009 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 47 2.26 - 2.92: 5760 2.92 - 3.58: 19254 3.58 - 4.24: 31090 4.24 - 4.90: 53322 Nonbonded interactions: 109473 Sorted by model distance: nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.606 2.450 nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 161 " model vdw 1.765 3.040 nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.774 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 161 " model vdw 1.797 3.040 nonbonded pdb=" ND2 ASN F 161 " pdb="CA CA F 602 " model vdw 1.817 3.330 ... (remaining 109468 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: 0.01 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' and (resid 41 through 101 or resid 108 through 703)) selection = chain 'D' selection = (chain 'G' and (resid 41 through 101 or resid 108 through 703)) 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 group one per residue 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: 0.990 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.005 0.043 13774 Z= 0.236 Angle : 0.641 9.927 18606 Z= 0.346 Chirality : 0.049 0.246 1912 Planarity : 0.004 0.039 2506 Dihedral : 17.386 87.297 5132 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.62 % Allowed : 20.71 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1646 helix: 0.42 (0.23), residues: 482 sheet: 1.10 (0.28), residues: 378 loop : -0.89 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 192 TYR 0.017 0.002 TYR C 76 PHE 0.027 0.002 PHE A 262 TRP 0.014 0.002 TRP E 67 HIS 0.029 0.002 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (13770) covalent geometry : angle 0.63924 / 0.35 (18598) SS BOND : bond 0.00183 / 0.10 ( 4) SS BOND : angle 2.30705 / 1.32 ( 8) hydrogen bonds : bond 0.16722 / 11.08 ( 641) hydrogen bonds : angle 6.88286 / 4.76 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 331 time to evaluate : 0.461 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: A 121 ASP cc_start: 0.8854 (t0) cc_final: 0.8639 (t0) REVERT: A 160 LYS cc_start: 0.8792 (mppt) cc_final: 0.8560 (mmtp) REVERT: A 207 TYR cc_start: 0.8812 (t80) cc_final: 0.8561 (t80) REVERT: B 58 VAL cc_start: 0.8659 (t) cc_final: 0.8361 (p) REVERT: B 107 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7922 (mp0) REVERT: B 178 HIS cc_start: 0.7260 (t-90) cc_final: 0.6950 (t-90) REVERT: B 351 GLN cc_start: 0.8558 (tp40) cc_final: 0.8131 (tt0) REVERT: D 74 LEU cc_start: 0.7632 (tp) cc_final: 0.7031 (tp) REVERT: D 119 ASN cc_start: 0.9248 (m110) cc_final: 0.8919 (m-40) REVERT: D 124 VAL cc_start: 0.9474 (t) cc_final: 0.9112 (t) REVERT: E 93 VAL cc_start: 0.9532 (t) cc_final: 0.9206 (p) REVERT: E 105 GLU cc_start: 0.8207 (tt0) cc_final: 0.8003 (tt0) REVERT: E 199 TYR cc_start: 0.8788 (m-80) cc_final: 0.8468 (m-10) REVERT: E 218 ASN cc_start: 0.8138 (m-40) cc_final: 0.7856 (p0) REVERT: G 115 ASP cc_start: 0.8817 (m-30) cc_final: 0.8487 (t0) REVERT: G 124 VAL cc_start: 0.8797 (t) cc_final: 0.8439 (p) REVERT: H 56 LEU cc_start: 0.8773 (pp) cc_final: 0.8115 (pt) REVERT: H 77 PHE cc_start: 0.8124 (t80) cc_final: 0.7918 (t80) REVERT: H 119 ASN cc_start: 0.8981 (m110) cc_final: 0.8771 (m-40) REVERT: F 56 HIS cc_start: 0.8198 (m-70) cc_final: 0.7935 (m-70) REVERT: F 137 VAL cc_start: 0.8326 (t) cc_final: 0.7866 (p) REVERT: F 207 TYR cc_start: 0.7945 (t80) cc_final: 0.7249 (t80) REVERT: F 208 TYR cc_start: 0.7520 (t80) cc_final: 0.7276 (t80) REVERT: F 306 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7817 (pm20) outliers start: 9 outliers final: 3 residues processed: 339 average time/residue: 0.1256 time to fit residues: 60.3571 Evaluate side-chains 247 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain F residue 306 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 359 GLN C 75 HIS C 80 HIS C 86 ASN D 51 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 338 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 80 HIS H 51 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN F 297 GLN F 359 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106658 restraints weight = 19933.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110997 restraints weight = 14158.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111453 restraints weight = 11242.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112054 restraints weight = 9956.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112313 restraints weight = 9910.112| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13774 Z= 0.151 Angle : 0.605 9.060 18606 Z= 0.317 Chirality : 0.047 0.240 1912 Planarity : 0.004 0.038 2506 Dihedral : 5.001 55.789 1793 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.46 % Allowed : 21.40 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1646 helix: 1.08 (0.23), residues: 492 sheet: 1.46 (0.28), residues: 338 loop : -1.08 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 126 TYR 0.023 0.002 TYR C 138 PHE 0.019 0.002 PHE B 52 TRP 0.010 0.001 TRP E 126 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (13770) covalent geometry : angle 0.60408 / 0.32 (18598) SS BOND : bond 0.00222 / 0.14 ( 4) SS BOND : angle 1.58311 / 0.89 ( 8) hydrogen bonds : bond 0.04395 / 2.82 ( 641) hydrogen bonds : angle 4.62460 / 3.18 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.551 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: A 350 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7766 (ptp90) REVERT: B 58 VAL cc_start: 0.8454 (t) cc_final: 0.8159 (p) REVERT: B 230 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7609 (t) REVERT: B 351 GLN cc_start: 0.8515 (tp40) cc_final: 0.8105 (tt0) REVERT: B 359 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: C 39 MET cc_start: 0.8567 (tpt) cc_final: 0.8357 (tpt) REVERT: C 99 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6488 (t70) REVERT: D 119 ASN cc_start: 0.9164 (m110) cc_final: 0.8900 (m-40) REVERT: E 93 VAL cc_start: 0.9311 (t) cc_final: 0.9032 (p) REVERT: E 199 TYR cc_start: 0.8577 (m-80) cc_final: 0.8239 (m-10) REVERT: E 289 TYR cc_start: 0.8671 (m-10) cc_final: 0.8321 (m-10) REVERT: E 323 PHE cc_start: 0.7447 (t80) cc_final: 0.7223 (t80) REVERT: E 350 ARG cc_start: 0.7933 (tmm-80) cc_final: 0.7476 (tmm-80) REVERT: G 73 GLN cc_start: 0.8531 (tt0) cc_final: 0.7717 (mm110) REVERT: G 93 LEU cc_start: 0.9079 (mt) cc_final: 0.8871 (mt) REVERT: G 99 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (t70) REVERT: H 73 GLN cc_start: 0.7936 (mt0) cc_final: 0.7637 (mm110) REVERT: H 77 PHE cc_start: 0.7944 (t80) cc_final: 0.7591 (t80) REVERT: H 119 ASN cc_start: 0.9394 (m110) cc_final: 0.9058 (m-40) REVERT: F 137 VAL cc_start: 0.8440 (t) cc_final: 0.8037 (p) outliers start: 50 outliers final: 19 residues processed: 312 average time/residue: 0.1199 time to fit residues: 54.5515 Evaluate side-chains 250 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 258 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 333 GLN A 338 GLN A 347 GLN A 351 GLN B 59 GLN B 359 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN F 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.166158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106190 restraints weight = 20101.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109444 restraints weight = 13216.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109961 restraints weight = 10878.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.110543 restraints weight = 9643.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111002 restraints weight = 9572.585| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13774 Z= 0.140 Angle : 0.610 13.918 18606 Z= 0.313 Chirality : 0.046 0.181 1912 Planarity : 0.003 0.043 2506 Dihedral : 4.589 58.926 1788 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.19 % Allowed : 22.58 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1646 helix: 1.37 (0.24), residues: 490 sheet: 1.34 (0.28), residues: 338 loop : -1.03 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.019 0.001 TYR C 138 PHE 0.033 0.001 PHE A 296 TRP 0.009 0.001 TRP F 126 HIS 0.023 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13770) covalent geometry : angle 0.60951 / 0.31 (18598) SS BOND : bond 0.00202 / 0.13 ( 4) SS BOND : angle 1.28457 / 0.71 ( 8) hydrogen bonds : bond 0.03970 / 2.57 ( 641) hydrogen bonds : angle 4.38205 / 3.04 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.539 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: A 355 ILE cc_start: 0.7996 (tt) cc_final: 0.7783 (tt) REVERT: A 362 TYR cc_start: 0.8420 (t80) cc_final: 0.8159 (t80) REVERT: B 58 VAL cc_start: 0.8540 (t) cc_final: 0.8238 (p) REVERT: B 230 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7630 (t) REVERT: B 351 GLN cc_start: 0.8481 (tp40) cc_final: 0.8027 (tt0) REVERT: C 67 MET cc_start: 0.7909 (mmt) cc_final: 0.7565 (mmp) REVERT: D 119 ASN cc_start: 0.9242 (m110) cc_final: 0.8937 (m-40) REVERT: D 124 VAL cc_start: 0.9098 (t) cc_final: 0.8684 (p) REVERT: D 128 ASP cc_start: 0.7827 (t70) cc_final: 0.7532 (m-30) REVERT: D 140 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: E 93 VAL cc_start: 0.9302 (t) cc_final: 0.9022 (p) REVERT: E 199 TYR cc_start: 0.8710 (m-80) cc_final: 0.8333 (m-10) REVERT: E 289 TYR cc_start: 0.8818 (m-10) cc_final: 0.8575 (m-10) REVERT: E 323 PHE cc_start: 0.7664 (t80) cc_final: 0.7390 (t80) REVERT: G 39 MET cc_start: 0.7316 (tpt) cc_final: 0.7111 (tpp) REVERT: G 73 GLN cc_start: 0.8582 (tt0) cc_final: 0.7732 (mm110) REVERT: G 99 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7820 (t70) REVERT: H 119 ASN cc_start: 0.9425 (m110) cc_final: 0.9087 (m-40) REVERT: F 56 HIS cc_start: 0.7688 (m-70) cc_final: 0.7352 (m170) REVERT: F 137 VAL cc_start: 0.8464 (t) cc_final: 0.8081 (p) REVERT: F 207 TYR cc_start: 0.8199 (t80) cc_final: 0.7557 (t80) REVERT: F 236 MET cc_start: 0.7727 (tpt) cc_final: 0.7474 (tpt) outliers start: 46 outliers final: 21 residues processed: 272 average time/residue: 0.1140 time to fit residues: 45.7612 Evaluate side-chains 237 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 0.0170 chunk 58 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 55 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN B 243 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 73 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108862 restraints weight = 19877.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107256 restraints weight = 14027.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107428 restraints weight = 12435.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108134 restraints weight = 12543.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108212 restraints weight = 11274.339| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13774 Z= 0.178 Angle : 0.633 10.792 18606 Z= 0.326 Chirality : 0.047 0.172 1912 Planarity : 0.004 0.046 2506 Dihedral : 4.615 59.552 1788 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.88 % Allowed : 22.78 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1646 helix: 1.44 (0.24), residues: 484 sheet: 1.13 (0.28), residues: 350 loop : -0.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 126 TYR 0.017 0.002 TYR C 138 PHE 0.027 0.002 PHE A 296 TRP 0.010 0.001 TRP F 126 HIS 0.008 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (13770) covalent geometry : angle 0.63160 / 0.33 (18598) SS BOND : bond 0.00147 / 0.09 ( 4) SS BOND : angle 1.82290 / 1.04 ( 8) hydrogen bonds : bond 0.03936 / 2.56 ( 641) hydrogen bonds : angle 4.33756 / 3.01 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: B 45 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7235 (tpt-90) REVERT: B 58 VAL cc_start: 0.8509 (t) cc_final: 0.8258 (p) REVERT: B 230 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7804 (t) REVERT: B 293 PHE cc_start: 0.8394 (t80) cc_final: 0.8109 (t80) REVERT: B 329 ARG cc_start: 0.7674 (ptp-110) cc_final: 0.7421 (ptp-110) REVERT: B 351 GLN cc_start: 0.8476 (tp40) cc_final: 0.8068 (tt0) REVERT: B 358 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 67 MET cc_start: 0.8005 (mmt) cc_final: 0.7702 (mmp) REVERT: D 75 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7895 (t70) REVERT: D 119 ASN cc_start: 0.9259 (m110) cc_final: 0.8913 (m-40) REVERT: D 124 VAL cc_start: 0.9125 (t) cc_final: 0.8798 (p) REVERT: D 140 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: E 199 TYR cc_start: 0.8717 (m-80) cc_final: 0.8355 (m-10) REVERT: E 289 TYR cc_start: 0.8932 (m-10) cc_final: 0.8520 (m-10) REVERT: E 323 PHE cc_start: 0.7748 (t80) cc_final: 0.7480 (t80) REVERT: G 138 TYR cc_start: 0.8365 (t80) cc_final: 0.8081 (t80) REVERT: H 119 ASN cc_start: 0.9405 (m110) cc_final: 0.9049 (m-40) REVERT: H 126 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8740 (ttp-110) REVERT: F 137 VAL cc_start: 0.8565 (t) cc_final: 0.8179 (p) outliers start: 56 outliers final: 32 residues processed: 265 average time/residue: 0.1104 time to fit residues: 42.9602 Evaluate side-chains 249 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 140 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN B 297 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN E 342 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.170100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113271 restraints weight = 19792.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114657 restraints weight = 15301.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115436 restraints weight = 12000.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115436 restraints weight = 11172.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115936 restraints weight = 10993.999| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13774 Z= 0.199 Angle : 0.640 8.953 18606 Z= 0.331 Chirality : 0.047 0.170 1912 Planarity : 0.004 0.048 2506 Dihedral : 4.713 59.810 1788 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.50 % Allowed : 22.58 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1646 helix: 1.48 (0.24), residues: 482 sheet: 0.89 (0.28), residues: 350 loop : -0.97 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.018 0.002 TYR A 207 PHE 0.022 0.002 PHE E 296 TRP 0.011 0.001 TRP F 67 HIS 0.012 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (13770) covalent geometry : angle 0.63921 / 0.33 (18598) SS BOND : bond 0.00198 / 0.13 ( 4) SS BOND : angle 1.68131 / 0.95 ( 8) hydrogen bonds : bond 0.03954 / 2.60 ( 641) hydrogen bonds : angle 4.36106 / 3.02 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 0.585 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: B 230 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7707 (t) REVERT: B 351 GLN cc_start: 0.8385 (tp40) cc_final: 0.8067 (tt0) REVERT: B 358 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 67 MET cc_start: 0.7883 (mmt) cc_final: 0.7615 (mmp) REVERT: D 119 ASN cc_start: 0.9108 (m110) cc_final: 0.8843 (m-40) REVERT: E 79 GLN cc_start: 0.8379 (pt0) cc_final: 0.8071 (pt0) REVERT: E 199 TYR cc_start: 0.8640 (m-80) cc_final: 0.8261 (m-10) REVERT: G 41 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7600 (mp) REVERT: G 73 GLN cc_start: 0.8498 (tt0) cc_final: 0.7698 (mm110) REVERT: G 138 TYR cc_start: 0.8243 (t80) cc_final: 0.8004 (t80) REVERT: H 119 ASN cc_start: 0.9282 (m110) cc_final: 0.8950 (m-40) REVERT: F 137 VAL cc_start: 0.8671 (t) cc_final: 0.8278 (p) outliers start: 65 outliers final: 39 residues processed: 267 average time/residue: 0.1140 time to fit residues: 44.8508 Evaluate side-chains 254 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 0.0020 chunk 123 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 GLN B 349 ASN C 55 HIS C 80 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.170065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111535 restraints weight = 19845.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114371 restraints weight = 14065.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117319 restraints weight = 11019.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116883 restraints weight = 10035.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116988 restraints weight = 9838.970| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13774 Z= 0.189 Angle : 0.656 12.745 18606 Z= 0.338 Chirality : 0.047 0.173 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.558 58.428 1786 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.16 % Allowed : 23.55 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1646 helix: 1.28 (0.24), residues: 494 sheet: 0.70 (0.27), residues: 362 loop : -0.91 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 126 TYR 0.021 0.002 TYR F 50 PHE 0.026 0.002 PHE E 296 TRP 0.011 0.001 TRP F 126 HIS 0.017 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (13770) covalent geometry : angle 0.65483 / 0.34 (18598) SS BOND : bond 0.00268 / 0.13 ( 4) SS BOND : angle 2.26673 / 1.31 ( 8) hydrogen bonds : bond 0.03996 / 2.63 ( 641) hydrogen bonds : angle 4.34785 / 3.01 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: B 230 CYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 351 GLN cc_start: 0.8404 (tp40) cc_final: 0.8074 (tt0) REVERT: B 358 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8289 (mm-30) REVERT: C 67 MET cc_start: 0.7854 (mmt) cc_final: 0.7597 (mmp) REVERT: C 79 MET cc_start: 0.8106 (ttm) cc_final: 0.7827 (ttp) REVERT: D 75 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7689 (t70) REVERT: D 119 ASN cc_start: 0.9116 (m110) cc_final: 0.8799 (m-40) REVERT: E 199 TYR cc_start: 0.8671 (m-80) cc_final: 0.8255 (m-10) REVERT: E 289 TYR cc_start: 0.8909 (m-10) cc_final: 0.8561 (m-10) REVERT: E 295 HIS cc_start: 0.8263 (m-70) cc_final: 0.8030 (m-70) REVERT: E 347 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7064 (tm-30) REVERT: G 41 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7675 (mp) REVERT: G 73 GLN cc_start: 0.8466 (tt0) cc_final: 0.7686 (mm110) REVERT: H 67 MET cc_start: 0.5428 (mmt) cc_final: 0.5207 (mmt) REVERT: H 119 ASN cc_start: 0.9306 (m110) cc_final: 0.8977 (m-40) REVERT: F 137 VAL cc_start: 0.8679 (t) cc_final: 0.8289 (p) outliers start: 60 outliers final: 40 residues processed: 267 average time/residue: 0.1115 time to fit residues: 43.9926 Evaluate side-chains 252 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 HIS C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 75 HIS E 131 GLN E 295 HIS E 342 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 86 ASN ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114019 restraints weight = 19795.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117884 restraints weight = 14339.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118459 restraints weight = 10404.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118252 restraints weight = 10418.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118564 restraints weight = 10385.224| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13774 Z= 0.139 Angle : 0.642 12.208 18606 Z= 0.333 Chirality : 0.046 0.176 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.477 56.334 1786 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.39 % Allowed : 23.96 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1646 helix: 1.38 (0.24), residues: 494 sheet: 0.84 (0.28), residues: 350 loop : -0.91 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.024 0.002 TYR F 50 PHE 0.022 0.001 PHE F 296 TRP 0.012 0.001 TRP F 126 HIS 0.015 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13770) covalent geometry : angle 0.64095 / 0.33 (18598) SS BOND : bond 0.00204 / 0.13 ( 4) SS BOND : angle 1.89060 / 1.07 ( 8) hydrogen bonds : bond 0.03653 / 2.40 ( 641) hydrogen bonds : angle 4.26913 / 2.97 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: B 50 TYR cc_start: 0.8672 (m-80) cc_final: 0.8428 (m-80) REVERT: B 230 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7504 (t) REVERT: B 351 GLN cc_start: 0.8434 (tp40) cc_final: 0.8101 (tt0) REVERT: B 358 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8312 (mm-30) REVERT: C 67 MET cc_start: 0.7902 (mmt) cc_final: 0.7615 (mmp) REVERT: C 79 MET cc_start: 0.8015 (ttm) cc_final: 0.7800 (ttp) REVERT: D 75 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7713 (t70) REVERT: D 119 ASN cc_start: 0.9139 (m110) cc_final: 0.8792 (m-40) REVERT: D 128 ASP cc_start: 0.7737 (t0) cc_final: 0.7110 (t0) REVERT: E 93 VAL cc_start: 0.9269 (t) cc_final: 0.8978 (p) REVERT: E 192 ARG cc_start: 0.8334 (mmt90) cc_final: 0.7951 (mmt90) REVERT: E 199 TYR cc_start: 0.8639 (m-80) cc_final: 0.8258 (m-10) REVERT: E 289 TYR cc_start: 0.8944 (m-10) cc_final: 0.8537 (m-10) REVERT: E 347 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7053 (tm-30) REVERT: G 41 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7651 (mp) REVERT: H 119 ASN cc_start: 0.9293 (m110) cc_final: 0.8971 (m-40) REVERT: F 137 VAL cc_start: 0.8633 (t) cc_final: 0.8241 (p) outliers start: 49 outliers final: 36 residues processed: 253 average time/residue: 0.1072 time to fit residues: 40.0824 Evaluate side-chains 250 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 55 HIS D 75 HIS ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120333 restraints weight = 19672.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119547 restraints weight = 13389.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119470 restraints weight = 11259.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120767 restraints weight = 11388.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120476 restraints weight = 10415.572| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13774 Z= 0.129 Angle : 0.656 16.205 18606 Z= 0.336 Chirality : 0.046 0.176 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.465 58.782 1786 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.53 % Allowed : 24.24 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1646 helix: 1.39 (0.24), residues: 492 sheet: 0.90 (0.28), residues: 350 loop : -0.94 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 350 TYR 0.027 0.002 TYR F 50 PHE 0.031 0.001 PHE E 296 TRP 0.012 0.001 TRP F 126 HIS 0.029 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13770) covalent geometry : angle 0.65546 / 0.34 (18598) SS BOND : bond 0.00154 / 0.10 ( 4) SS BOND : angle 1.61732 / 0.90 ( 8) hydrogen bonds : bond 0.03502 / 2.31 ( 641) hydrogen bonds : angle 4.21174 / 2.93 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: A 292 GLU cc_start: 0.8600 (pt0) cc_final: 0.8202 (pt0) REVERT: B 230 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7508 (t) REVERT: B 351 GLN cc_start: 0.8416 (tp40) cc_final: 0.8127 (tt0) REVERT: B 358 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 53 MET cc_start: 0.8687 (mmm) cc_final: 0.7755 (mmm) REVERT: D 119 ASN cc_start: 0.9093 (m110) cc_final: 0.8750 (m-40) REVERT: D 143 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8604 (mmtt) REVERT: E 93 VAL cc_start: 0.9277 (t) cc_final: 0.9019 (p) REVERT: E 192 ARG cc_start: 0.8276 (mmt90) cc_final: 0.8027 (mmt90) REVERT: E 199 TYR cc_start: 0.8662 (m-80) cc_final: 0.8269 (m-10) REVERT: E 289 TYR cc_start: 0.8870 (m-10) cc_final: 0.8457 (m-10) REVERT: E 347 GLN cc_start: 0.7663 (tp-100) cc_final: 0.6960 (tm-30) REVERT: G 127 ASP cc_start: 0.7796 (t0) cc_final: 0.7537 (t0) REVERT: H 119 ASN cc_start: 0.9226 (m110) cc_final: 0.8914 (m-40) REVERT: F 137 VAL cc_start: 0.8591 (t) cc_final: 0.8208 (p) outliers start: 51 outliers final: 33 residues processed: 261 average time/residue: 0.1117 time to fit residues: 43.3748 Evaluate side-chains 248 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 148 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN A 338 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 75 HIS E 131 GLN E 342 HIS G 75 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 342 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113381 restraints weight = 19917.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112910 restraints weight = 13580.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113407 restraints weight = 11043.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113832 restraints weight = 10836.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114075 restraints weight = 10328.151| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13774 Z= 0.277 Angle : 0.745 14.835 18606 Z= 0.391 Chirality : 0.050 0.184 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.882 57.423 1786 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.25 % Allowed : 25.07 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1646 helix: 1.06 (0.24), residues: 506 sheet: 0.47 (0.27), residues: 362 loop : -1.04 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 126 TYR 0.023 0.002 TYR F 50 PHE 0.042 0.002 PHE E 323 TRP 0.010 0.001 TRP F 126 HIS 0.014 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 (13770) covalent geometry : angle 0.74343 / 0.39 (18598) SS BOND : bond 0.00132 / 0.06 ( 4) SS BOND : angle 2.12647 / 1.19 ( 8) hydrogen bonds : bond 0.04392 / 2.88 ( 641) hydrogen bonds : angle 4.61984 / 3.19 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.523 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: A 78 ASP cc_start: 0.8155 (t0) cc_final: 0.7842 (t0) REVERT: A 79 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: B 351 GLN cc_start: 0.8499 (tp40) cc_final: 0.8195 (tt0) REVERT: B 358 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 49 GLN cc_start: 0.9443 (tp-100) cc_final: 0.8536 (tp-100) REVERT: D 49 GLN cc_start: 0.8447 (tp-100) cc_final: 0.8145 (tm-30) REVERT: D 52 ILE cc_start: 0.9232 (mp) cc_final: 0.9010 (tt) REVERT: D 53 MET cc_start: 0.8735 (mmm) cc_final: 0.8286 (mmm) REVERT: D 76 TYR cc_start: 0.8309 (t80) cc_final: 0.8096 (t80) REVERT: D 119 ASN cc_start: 0.9097 (m110) cc_final: 0.8742 (m-40) REVERT: D 143 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8667 (mmtp) REVERT: E 199 TYR cc_start: 0.8734 (m-80) cc_final: 0.8341 (m-10) REVERT: E 289 TYR cc_start: 0.8886 (m-10) cc_final: 0.8497 (m-10) REVERT: H 85 ASN cc_start: 0.8768 (p0) cc_final: 0.8395 (p0) REVERT: H 86 ASN cc_start: 0.8834 (m-40) cc_final: 0.8511 (m110) REVERT: H 119 ASN cc_start: 0.9234 (m110) cc_final: 0.8942 (m-40) REVERT: F 137 VAL cc_start: 0.8793 (t) cc_final: 0.8382 (p) outliers start: 47 outliers final: 36 residues processed: 241 average time/residue: 0.1170 time to fit residues: 41.4349 Evaluate side-chains 236 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 75 HIS E 131 GLN E 342 HIS G 75 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.170709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114545 restraints weight = 19724.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116229 restraints weight = 14805.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117456 restraints weight = 11647.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117531 restraints weight = 10568.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117856 restraints weight = 10404.100| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13774 Z= 0.160 Angle : 0.710 16.221 18606 Z= 0.370 Chirality : 0.048 0.184 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.762 58.705 1786 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.49 % Allowed : 25.90 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1646 helix: 1.13 (0.24), residues: 504 sheet: 0.54 (0.27), residues: 362 loop : -0.99 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.030 0.002 TYR H 138 PHE 0.023 0.002 PHE E 296 TRP 0.013 0.001 TRP F 126 HIS 0.012 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13770) covalent geometry : angle 0.70758 / 0.37 (18598) SS BOND : bond 0.00249 / 0.17 ( 4) SS BOND : angle 2.69400 / 1.52 ( 8) hydrogen bonds : bond 0.03883 / 2.53 ( 641) hydrogen bonds : angle 4.47936 / 3.13 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.419 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: A 79 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8477 (pt0) REVERT: B 351 GLN cc_start: 0.8462 (tp40) cc_final: 0.8181 (tt0) REVERT: B 358 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 49 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8877 (tp-100) REVERT: D 53 MET cc_start: 0.8629 (mmm) cc_final: 0.8359 (mmm) REVERT: D 73 GLN cc_start: 0.7442 (pt0) cc_final: 0.6932 (pp30) REVERT: D 119 ASN cc_start: 0.9012 (m110) cc_final: 0.8659 (m-40) REVERT: D 143 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8559 (mmtp) REVERT: E 199 TYR cc_start: 0.8638 (m-80) cc_final: 0.8294 (m-10) REVERT: E 289 TYR cc_start: 0.8810 (m-10) cc_final: 0.8438 (m-10) REVERT: G 127 ASP cc_start: 0.7658 (t0) cc_final: 0.7441 (t0) REVERT: H 85 ASN cc_start: 0.8674 (p0) cc_final: 0.8292 (p0) REVERT: H 86 ASN cc_start: 0.8759 (m-40) cc_final: 0.8415 (m110) REVERT: H 119 ASN cc_start: 0.9190 (m110) cc_final: 0.8898 (m-40) REVERT: F 137 VAL cc_start: 0.8666 (t) cc_final: 0.8306 (p) outliers start: 36 outliers final: 33 residues processed: 241 average time/residue: 0.1105 time to fit residues: 39.4393 Evaluate side-chains 239 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN E 342 HIS G 75 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.168019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112086 restraints weight = 19948.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112813 restraints weight = 14064.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113691 restraints weight = 11257.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113831 restraints weight = 10620.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113939 restraints weight = 10418.341| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13774 Z= 0.259 Angle : 0.767 15.186 18606 Z= 0.400 Chirality : 0.050 0.206 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.910 55.900 1786 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.77 % Allowed : 25.69 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1646 helix: 1.08 (0.24), residues: 504 sheet: 0.33 (0.28), residues: 362 loop : -1.13 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 126 TYR 0.031 0.002 TYR H 138 PHE 0.024 0.002 PHE A 262 TRP 0.010 0.001 TRP F 126 HIS 0.013 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (13770) covalent geometry : angle 0.76497 / 0.40 (18598) SS BOND : bond 0.00254 / 0.17 ( 4) SS BOND : angle 2.96494 / 1.64 ( 8) hydrogen bonds : bond 0.04289 / 2.82 ( 641) hydrogen bonds : angle 4.69730 / 3.26 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2342.91 seconds wall clock time: 41 minutes 14.69 seconds (2474.69 seconds total)