Starting phenix.real_space_refine on Wed Mar 4 14:29:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn4_27554/03_2026/8dn4_27554_trim.cif" } resolution = 4.1 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= 0.010 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9031 2.51 5 N 2234 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13817 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2770 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2723 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2745 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2728 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {'HEX': 2, 'LNK': 1, 'NAG': 1, 'NBU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'HEX': 3, 'NAG': 1, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {'HEX': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Unusual residues: {'DD9': 1, 'HEX': 1, 'NAG': 1, 'NBU': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'HEX': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.24 Number of scatterers: 13817 At special positions: 0 Unit cell: (101.26, 122.84, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2452 8.00 N 2234 7.00 C 9031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 709.5 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 22 sheets defined 41.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.761A pdb=" N SER D 22 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY D 23 " --> pdb=" O ARG D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 23' Processing helix chain 'D' and resid 52 through 55 removed outlier: 3.608A pdb=" N THR D 55 " --> pdb=" O ALA D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 5.028A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 244 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 274 removed outlier: 4.258A pdb=" N ARG D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 311 removed outlier: 4.719A pdb=" N HIS D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 418 Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.791A pdb=" N SER A 22 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.671A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 271 removed outlier: 4.387A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.640A pdb=" N TRP A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 417 Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 4.016A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 244 removed outlier: 3.526A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 274 removed outlier: 3.581A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.825A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 418 removed outlier: 3.975A pdb=" N ARG B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.624A pdb=" N SER C 22 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 23 " --> pdb=" O ARG C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 4.058A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 Proline residue: C 230 - end of helix removed outlier: 3.805A pdb=" N TRP C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 274 removed outlier: 3.653A pdb=" N LEU C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 310 removed outlier: 3.882A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 417 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 43 removed outlier: 4.638A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 109 through 116 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 267 Processing helix chain 'E' and resid 275 through 296 Processing helix chain 'E' and resid 305 through 333 Processing helix chain 'E' and resid 447 through 475 removed outlier: 4.310A pdb=" N ILE E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.771A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 133 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.771A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 65 " --> pdb=" O ASN D 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.695A pdb=" N ALA D 212 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AA5, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.525A pdb=" N TYR A 128 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.557A pdb=" N ALA A 212 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU A 211 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP A 194 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG A 213 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU A 192 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS A 215 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AB1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.576A pdb=" N LEU B 85 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.567A pdb=" N CYS B 152 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 212 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS B 209 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG B 196 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU B 211 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP B 194 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG B 213 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU B 192 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS B 215 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 188 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 200 through 202 removed outlier: 4.001A pdb=" N LYS B 200 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 207 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 40 through 47 removed outlier: 3.608A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 47 removed outlier: 3.608A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.722A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 200 through 202 removed outlier: 4.005A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.971A pdb=" N ILE E 83 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 85 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 152 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 126 through 129 removed outlier: 7.430A pdb=" N THR E 158 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA E 129 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N SER E 156 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 85 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE E 83 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.591A pdb=" N PHE E 122 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 180 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.711A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1932 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: 2.38 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2792 1.33 - 1.45: 3462 1.45 - 1.58: 7725 1.58 - 1.70: 1 1.70 - 1.83: 168 Bond restraints: 14148 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N GLN D 150 " pdb=" CA GLN D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N CYS D 152 " pdb=" CA CYS D 152 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.68e+00 bond pdb=" N ILE D 153 " pdb=" CA ILE D 153 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.22e+00 ... (remaining 14143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 18312 1.52 - 3.04: 654 3.04 - 4.56: 109 4.56 - 6.08: 54 6.08 - 7.60: 15 Bond angle restraints: 19144 Sorted by residual: angle pdb=" N LYS B 418 " pdb=" CA LYS B 418 " pdb=" C LYS B 418 " ideal model delta sigma weight residual 112.94 106.45 6.49 1.41e+00 5.03e-01 2.12e+01 angle pdb=" N LEU E 167 " pdb=" CA LEU E 167 " pdb=" C LEU E 167 " ideal model delta sigma weight residual 111.24 105.41 5.83 1.38e+00 5.25e-01 1.79e+01 angle pdb=" CA PRO B 146 " pdb=" N PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" N THR B 113 " pdb=" CA THR B 113 " pdb=" CB THR B 113 " ideal model delta sigma weight residual 111.57 117.45 -5.88 1.68e+00 3.54e-01 1.23e+01 angle pdb=" C LEU E 464 " pdb=" N PHE E 465 " pdb=" CA PHE E 465 " ideal model delta sigma weight residual 120.72 115.10 5.62 1.67e+00 3.59e-01 1.13e+01 ... (remaining 19139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 8132 24.60 - 49.20: 331 49.20 - 73.80: 28 73.80 - 98.39: 8 98.39 - 122.99: 9 Dihedral angle restraints: 8508 sinusoidal: 3542 harmonic: 4966 Sorted by residual: dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA CYS B 209 " pdb=" C CYS B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 209 " pdb=" CB CYS B 209 " ideal model delta sinusoidal sigma weight residual -86.00 -51.22 -34.78 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1946 0.084 - 0.167: 178 0.167 - 0.251: 11 0.251 - 0.335: 1 0.335 - 0.418: 2 Chirality restraints: 2138 Sorted by residual: chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 38 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2135 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 239 " 0.028 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP B 239 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 239 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 239 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 239 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 239 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 239 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 239 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 239 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 145 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO B 146 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 196 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C ARG B 196 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG B 196 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 197 " -0.017 2.00e-02 2.50e+03 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 3 2.06 - 2.77: 2590 2.77 - 3.48: 20795 3.48 - 4.19: 31774 4.19 - 4.90: 54188 Nonbonded interactions: 109350 Sorted by model distance: nonbonded pdb=" CD2 LEU D 261 " pdb=" CZ PHE E 282 " model vdw 1.353 3.760 nonbonded pdb=" CG LEU D 261 " pdb=" CZ PHE E 282 " model vdw 1.990 3.770 nonbonded pdb=" CG2 THR A 258 " pdb=" CD1 LEU E 285 " model vdw 2.036 3.880 nonbonded pdb=" O SER E 262 " pdb=" OG SER E 265 " model vdw 2.096 3.040 nonbonded pdb=" O VAL B 235 " pdb=" OG SER B 238 " model vdw 2.112 3.040 ... (remaining 109345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 309 or (resid 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 501)) selection = (chain 'B' and (resid 8 through 309 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 501)) selection = (chain 'C' and (resid 8 through 309 or resid 387 through 501)) selection = (chain 'D' and (resid 8 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 309 or (resid 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 501)) } 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: 1.570 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.088 14163 Z= 0.184 Angle : 0.731 8.385 19179 Z= 0.380 Chirality : 0.049 0.418 2138 Planarity : 0.005 0.115 2386 Dihedral : 13.547 122.993 5260 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 0.40 % Allowed : 0.46 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1662 helix: 1.93 (0.22), residues: 578 sheet: -0.82 (0.31), residues: 302 loop : -1.61 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 29 TYR 0.021 0.001 TYR D 413 PHE 0.035 0.002 PHE D 412 TRP 0.075 0.002 TRP B 239 HIS 0.001 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00360 (14148) covalent geometry : angle 0.72294 (19144) SS BOND : bond 0.00287 ( 10) SS BOND : angle 2.51791 ( 20) hydrogen bonds : bond 0.18017 ( 653) hydrogen bonds : angle 6.73904 ( 1932) link_NAG-ASN : bond 0.00661 ( 5) link_NAG-ASN : angle 2.78166 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 421 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 ASP cc_start: 0.9001 (t0) cc_final: 0.7855 (t0) REVERT: D 287 MET cc_start: 0.9100 (mmm) cc_final: 0.8812 (mmm) REVERT: D 311 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6555 (m90) REVERT: D 404 MET cc_start: 0.8569 (tmm) cc_final: 0.8304 (tmm) REVERT: D 408 ILE cc_start: 0.9260 (tp) cc_final: 0.8953 (tp) REVERT: A 155 GLN cc_start: 0.8607 (mt0) cc_final: 0.8282 (mt0) REVERT: A 186 GLN cc_start: 0.8769 (mt0) cc_final: 0.8551 (mt0) REVERT: A 211 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 217 GLU cc_start: 0.8367 (mp0) cc_final: 0.8012 (mp0) REVERT: A 220 MET cc_start: 0.7656 (pmm) cc_final: 0.7354 (pmm) REVERT: A 274 LEU cc_start: 0.9497 (mp) cc_final: 0.9107 (tt) REVERT: A 287 MET cc_start: 0.9112 (mmm) cc_final: 0.8523 (mmm) REVERT: B 211 GLU cc_start: 0.7716 (pm20) cc_final: 0.7114 (pm20) REVERT: B 220 MET cc_start: 0.8484 (pmm) cc_final: 0.8198 (pmm) REVERT: B 239 TRP cc_start: 0.8157 (m-90) cc_final: 0.6994 (m-90) REVERT: C 90 LEU cc_start: 0.9431 (tp) cc_final: 0.8778 (tp) REVERT: C 97 ASP cc_start: 0.7122 (p0) cc_final: 0.6523 (p0) REVERT: C 98 LEU cc_start: 0.8964 (tp) cc_final: 0.8663 (tp) REVERT: C 103 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 112 THR cc_start: 0.9400 (p) cc_final: 0.9198 (p) REVERT: C 128 TYR cc_start: 0.8988 (t80) cc_final: 0.8745 (t80) REVERT: C 167 ILE cc_start: 0.7644 (tt) cc_final: 0.7314 (tt) REVERT: C 239 TRP cc_start: 0.7449 (m-10) cc_final: 0.6858 (m-10) REVERT: C 411 MET cc_start: 0.7074 (tpt) cc_final: 0.6752 (mmp) REVERT: C 414 TRP cc_start: 0.8813 (m100) cc_final: 0.8599 (m100) REVERT: E 115 CYS cc_start: 0.8812 (t) cc_final: 0.8612 (t) REVERT: E 170 MET cc_start: 0.8276 (mmm) cc_final: 0.8012 (mmm) REVERT: E 173 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6683 (mm110) REVERT: E 176 LYS cc_start: 0.8995 (ptmm) cc_final: 0.8341 (pttt) REVERT: E 314 CYS cc_start: 0.9327 (m) cc_final: 0.9037 (m) REVERT: E 324 GLU cc_start: 0.8080 (pp20) cc_final: 0.7772 (mm-30) outliers start: 6 outliers final: 2 residues processed: 425 average time/residue: 0.0979 time to fit residues: 64.4646 Evaluate side-chains 326 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 323 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 177 GLN A 107 HIS A 171 GLN A 177 GLN A 215 HIS C 61 ASN C 102 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094887 restraints weight = 37201.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097965 restraints weight = 20126.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100034 restraints weight = 13139.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101392 restraints weight = 9761.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102333 restraints weight = 7985.521| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14163 Z= 0.138 Angle : 0.693 10.422 19179 Z= 0.352 Chirality : 0.047 0.317 2138 Planarity : 0.005 0.073 2386 Dihedral : 9.325 110.472 1981 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 0.27 % Allowed : 4.58 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1662 helix: 1.78 (0.22), residues: 567 sheet: -0.70 (0.30), residues: 310 loop : -1.58 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 29 TYR 0.013 0.001 TYR D 413 PHE 0.026 0.002 PHE A 242 TRP 0.031 0.001 TRP B 239 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00303 (14148) covalent geometry : angle 0.68557 (19144) SS BOND : bond 0.00658 ( 10) SS BOND : angle 2.48819 ( 20) hydrogen bonds : bond 0.04391 ( 653) hydrogen bonds : angle 5.13598 ( 1932) link_NAG-ASN : bond 0.00516 ( 5) link_NAG-ASN : angle 2.52795 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 392 time to evaluate : 0.519 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: D 17 LEU cc_start: 0.9297 (tp) cc_final: 0.8616 (tp) REVERT: D 18 MET cc_start: 0.9137 (pmm) cc_final: 0.8836 (pmm) REVERT: D 89 MET cc_start: 0.9360 (mmm) cc_final: 0.9028 (mpp) REVERT: D 141 ASP cc_start: 0.8915 (t0) cc_final: 0.8696 (t0) REVERT: D 148 ASP cc_start: 0.8707 (t0) cc_final: 0.8474 (t0) REVERT: D 149 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8664 (p) REVERT: D 211 GLU cc_start: 0.7584 (tp30) cc_final: 0.7172 (tp30) REVERT: D 217 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 404 MET cc_start: 0.8512 (tmm) cc_final: 0.8214 (tmm) REVERT: D 408 ILE cc_start: 0.9291 (tp) cc_final: 0.9045 (tp) REVERT: D 412 PHE cc_start: 0.8486 (m-80) cc_final: 0.8216 (m-10) REVERT: A 107 HIS cc_start: 0.8423 (p90) cc_final: 0.8005 (p90) REVERT: A 155 GLN cc_start: 0.8366 (mt0) cc_final: 0.7931 (mt0) REVERT: A 211 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 220 MET cc_start: 0.7379 (pmm) cc_final: 0.7126 (pmm) REVERT: A 262 THR cc_start: 0.9461 (p) cc_final: 0.8721 (p) REVERT: A 274 LEU cc_start: 0.9516 (mp) cc_final: 0.9144 (tt) REVERT: A 287 MET cc_start: 0.9206 (mmm) cc_final: 0.8569 (mmm) REVERT: B 17 LEU cc_start: 0.9310 (tp) cc_final: 0.8778 (tp) REVERT: B 57 ASP cc_start: 0.8268 (p0) cc_final: 0.7977 (p0) REVERT: B 66 GLN cc_start: 0.9009 (mp-120) cc_final: 0.8777 (mp10) REVERT: B 173 GLN cc_start: 0.8936 (mp10) cc_final: 0.8533 (mp10) REVERT: B 211 GLU cc_start: 0.7486 (pm20) cc_final: 0.6581 (pm20) REVERT: B 235 VAL cc_start: 0.9585 (p) cc_final: 0.8783 (p) REVERT: B 239 TRP cc_start: 0.8265 (m-90) cc_final: 0.6935 (m-90) REVERT: C 17 LEU cc_start: 0.9283 (tp) cc_final: 0.8997 (tp) REVERT: C 18 MET cc_start: 0.8736 (pmm) cc_final: 0.8125 (pmm) REVERT: C 97 ASP cc_start: 0.7537 (p0) cc_final: 0.6854 (p0) REVERT: C 98 LEU cc_start: 0.9028 (tp) cc_final: 0.8809 (tp) REVERT: C 103 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 153 ILE cc_start: 0.8979 (pt) cc_final: 0.8657 (pt) REVERT: C 167 ILE cc_start: 0.7608 (tt) cc_final: 0.7140 (tt) REVERT: C 239 TRP cc_start: 0.7654 (m-10) cc_final: 0.7307 (m-10) REVERT: C 404 MET cc_start: 0.8675 (ttt) cc_final: 0.8140 (tpp) REVERT: C 411 MET cc_start: 0.6863 (tpt) cc_final: 0.6549 (mmp) REVERT: C 414 TRP cc_start: 0.8879 (m100) cc_final: 0.8444 (m100) REVERT: E 74 GLU cc_start: 0.8478 (mp0) cc_final: 0.8166 (mp0) REVERT: E 115 CYS cc_start: 0.8798 (t) cc_final: 0.8584 (t) REVERT: E 155 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8911 (pp) REVERT: E 170 MET cc_start: 0.8330 (mmm) cc_final: 0.8033 (mmm) REVERT: E 173 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6668 (mm110) REVERT: E 176 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8370 (pttt) REVERT: E 314 CYS cc_start: 0.9348 (m) cc_final: 0.8767 (m) outliers start: 4 outliers final: 0 residues processed: 395 average time/residue: 0.0954 time to fit residues: 59.1250 Evaluate side-chains 329 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 150 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 177 GLN C 61 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090983 restraints weight = 37314.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093862 restraints weight = 20410.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095797 restraints weight = 13494.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097085 restraints weight = 10124.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097861 restraints weight = 8342.333| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14163 Z= 0.245 Angle : 0.728 11.415 19179 Z= 0.375 Chirality : 0.047 0.307 2138 Planarity : 0.005 0.057 2386 Dihedral : 8.395 110.176 1981 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.50 (0.21), residues: 1662 helix: 1.71 (0.22), residues: 575 sheet: -0.93 (0.29), residues: 317 loop : -1.69 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 29 TYR 0.016 0.002 TYR E 224 PHE 0.042 0.002 PHE E 282 TRP 0.013 0.002 TRP D 414 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00554 (14148) covalent geometry : angle 0.72371 (19144) SS BOND : bond 0.00393 ( 10) SS BOND : angle 1.61299 ( 20) hydrogen bonds : bond 0.04668 ( 653) hydrogen bonds : angle 5.04072 ( 1932) link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 2.40579 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.519 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: D 138 CYS cc_start: 0.6655 (t) cc_final: 0.6321 (t) REVERT: D 404 MET cc_start: 0.8434 (tmm) cc_final: 0.8123 (tmm) REVERT: D 408 ILE cc_start: 0.9255 (tp) cc_final: 0.8998 (tp) REVERT: D 412 PHE cc_start: 0.8488 (m-80) cc_final: 0.8128 (m-10) REVERT: A 107 HIS cc_start: 0.8905 (p90) cc_final: 0.8405 (p-80) REVERT: A 220 MET cc_start: 0.7471 (pmm) cc_final: 0.7248 (pmm) REVERT: A 246 MET cc_start: 0.9352 (ppp) cc_final: 0.8809 (ppp) REVERT: A 274 LEU cc_start: 0.9533 (mp) cc_final: 0.9155 (tt) REVERT: A 287 MET cc_start: 0.9194 (mmm) cc_final: 0.8583 (mmm) REVERT: B 17 LEU cc_start: 0.9328 (tp) cc_final: 0.8944 (tp) REVERT: B 103 GLU cc_start: 0.7949 (pp20) cc_final: 0.7539 (pp20) REVERT: B 110 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7438 (pt0) REVERT: B 186 GLN cc_start: 0.8451 (pm20) cc_final: 0.8039 (pm20) REVERT: B 211 GLU cc_start: 0.7274 (pm20) cc_final: 0.7017 (pm20) REVERT: B 220 MET cc_start: 0.7935 (pmm) cc_final: 0.7587 (pmm) REVERT: B 226 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 242 PHE cc_start: 0.8101 (m-80) cc_final: 0.7735 (m-80) REVERT: C 15 ASP cc_start: 0.8394 (t0) cc_final: 0.8138 (t0) REVERT: C 17 LEU cc_start: 0.9310 (tp) cc_final: 0.8918 (tp) REVERT: C 18 MET cc_start: 0.8719 (pmm) cc_final: 0.8024 (pmm) REVERT: C 97 ASP cc_start: 0.7808 (p0) cc_final: 0.7147 (p0) REVERT: C 103 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 167 ILE cc_start: 0.7855 (tt) cc_final: 0.7415 (tt) REVERT: C 238 SER cc_start: 0.8248 (p) cc_final: 0.7981 (p) REVERT: C 239 TRP cc_start: 0.7686 (m-10) cc_final: 0.6822 (m-10) REVERT: C 283 ILE cc_start: 0.8193 (tt) cc_final: 0.7096 (tp) REVERT: C 404 MET cc_start: 0.8653 (ttt) cc_final: 0.8036 (tpp) REVERT: C 411 MET cc_start: 0.6772 (tpt) cc_final: 0.6351 (mmp) REVERT: C 414 TRP cc_start: 0.8994 (m100) cc_final: 0.8481 (m100) REVERT: E 77 MET cc_start: 0.8304 (tpp) cc_final: 0.8056 (tpp) REVERT: E 115 CYS cc_start: 0.8777 (t) cc_final: 0.8557 (t) REVERT: E 125 ASN cc_start: 0.8640 (m110) cc_final: 0.8246 (m110) REVERT: E 173 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7472 (mm110) REVERT: E 176 LYS cc_start: 0.9100 (ptmm) cc_final: 0.8387 (pttt) REVERT: E 200 GLN cc_start: 0.8703 (mp10) cc_final: 0.8420 (mp-120) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.0989 time to fit residues: 57.5087 Evaluate side-chains 298 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS A 61 ASN A 150 GLN A 171 GLN A 177 GLN A 186 GLN C 61 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN E 329 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093216 restraints weight = 37021.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096241 restraints weight = 19980.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098250 restraints weight = 13069.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099598 restraints weight = 9729.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100395 restraints weight = 7957.923| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14163 Z= 0.171 Angle : 0.696 10.334 19179 Z= 0.352 Chirality : 0.046 0.303 2138 Planarity : 0.005 0.053 2386 Dihedral : 7.835 108.652 1981 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 0.27 % Allowed : 3.72 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.21), residues: 1662 helix: 1.69 (0.22), residues: 576 sheet: -0.83 (0.30), residues: 314 loop : -1.65 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 252 TYR 0.029 0.001 TYR A 301 PHE 0.037 0.002 PHE E 282 TRP 0.052 0.002 TRP B 239 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00390 (14148) covalent geometry : angle 0.69086 (19144) SS BOND : bond 0.00274 ( 10) SS BOND : angle 1.81241 ( 20) hydrogen bonds : bond 0.04302 ( 653) hydrogen bonds : angle 4.83353 ( 1932) link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 2.53972 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9148 (t0) cc_final: 0.8818 (t0) REVERT: D 226 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8833 (tm-30) REVERT: D 311 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6240 (m-70) REVERT: D 404 MET cc_start: 0.8441 (tmm) cc_final: 0.8110 (tmm) REVERT: D 408 ILE cc_start: 0.9220 (tp) cc_final: 0.8882 (tp) REVERT: D 412 PHE cc_start: 0.8447 (m-80) cc_final: 0.8211 (m-80) REVERT: A 107 HIS cc_start: 0.8834 (p90) cc_final: 0.8025 (p90) REVERT: A 220 MET cc_start: 0.7422 (pmm) cc_final: 0.7138 (pmm) REVERT: A 274 LEU cc_start: 0.9512 (mp) cc_final: 0.9156 (tt) REVERT: A 287 MET cc_start: 0.9260 (mmm) cc_final: 0.8609 (mmm) REVERT: A 306 PHE cc_start: 0.8629 (t80) cc_final: 0.8246 (t80) REVERT: B 97 ASP cc_start: 0.8099 (p0) cc_final: 0.7539 (p0) REVERT: B 103 GLU cc_start: 0.7891 (pp20) cc_final: 0.7484 (pp20) REVERT: B 110 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7342 (pt0) REVERT: B 142 LEU cc_start: 0.9398 (mp) cc_final: 0.9130 (mp) REVERT: B 157 GLU cc_start: 0.8309 (pt0) cc_final: 0.7663 (pt0) REVERT: B 220 MET cc_start: 0.7925 (pmm) cc_final: 0.7611 (pmm) REVERT: B 226 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 239 TRP cc_start: 0.8294 (m-90) cc_final: 0.6941 (m-90) REVERT: B 242 PHE cc_start: 0.7992 (m-80) cc_final: 0.7746 (m-80) REVERT: B 279 TYR cc_start: 0.7927 (p90) cc_final: 0.7241 (p90) REVERT: C 15 ASP cc_start: 0.8431 (t0) cc_final: 0.8124 (t0) REVERT: C 17 LEU cc_start: 0.9283 (tp) cc_final: 0.8885 (tp) REVERT: C 18 MET cc_start: 0.8760 (pmm) cc_final: 0.8057 (pmm) REVERT: C 78 TYR cc_start: 0.7146 (m-10) cc_final: 0.6868 (m-10) REVERT: C 97 ASP cc_start: 0.7771 (p0) cc_final: 0.7069 (p0) REVERT: C 102 ASN cc_start: 0.8383 (p0) cc_final: 0.7758 (p0) REVERT: C 103 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 404 MET cc_start: 0.8689 (ttt) cc_final: 0.8069 (tpp) REVERT: C 414 TRP cc_start: 0.8951 (m100) cc_final: 0.8448 (m100) REVERT: E 77 MET cc_start: 0.8271 (tpp) cc_final: 0.8008 (tpp) REVERT: E 115 CYS cc_start: 0.8683 (t) cc_final: 0.8449 (t) REVERT: E 170 MET cc_start: 0.8409 (mmm) cc_final: 0.8172 (mmm) REVERT: E 173 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7112 (mm110) REVERT: E 200 GLN cc_start: 0.8680 (mp10) cc_final: 0.8310 (mp-120) REVERT: E 235 GLU cc_start: 0.7663 (tm-30) cc_final: 0.6815 (tm-30) REVERT: E 310 TRP cc_start: 0.9248 (t-100) cc_final: 0.8993 (t-100) REVERT: E 465 PHE cc_start: 0.8327 (p90) cc_final: 0.7302 (p90) outliers start: 4 outliers final: 0 residues processed: 375 average time/residue: 0.0996 time to fit residues: 57.9894 Evaluate side-chains 314 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 0.0060 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 122 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN A 61 ASN A 171 GLN A 186 GLN ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 115 ASN ** 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 = 0.3699 r_free = 0.3699 target = 0.115893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094004 restraints weight = 37172.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097056 restraints weight = 20257.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099081 restraints weight = 13261.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100447 restraints weight = 9882.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101370 restraints weight = 8072.922| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14163 Z= 0.148 Angle : 0.686 9.756 19179 Z= 0.348 Chirality : 0.046 0.330 2138 Planarity : 0.004 0.043 2386 Dihedral : 7.804 106.989 1981 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.08 % Favored : 93.74 % Rotamer: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1662 helix: 1.74 (0.22), residues: 577 sheet: -0.66 (0.31), residues: 309 loop : -1.61 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 29 TYR 0.022 0.001 TYR A 301 PHE 0.034 0.002 PHE C 402 TRP 0.022 0.001 TRP B 239 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00338 (14148) covalent geometry : angle 0.67849 (19144) SS BOND : bond 0.00917 ( 10) SS BOND : angle 2.64815 ( 20) hydrogen bonds : bond 0.04098 ( 653) hydrogen bonds : angle 4.73011 ( 1932) link_NAG-ASN : bond 0.00287 ( 5) link_NAG-ASN : angle 2.31677 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.560 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: D 141 ASP cc_start: 0.9057 (t0) cc_final: 0.8814 (t0) REVERT: D 196 ARG cc_start: 0.8357 (ptt180) cc_final: 0.8103 (ptt90) REVERT: D 287 MET cc_start: 0.9164 (mmm) cc_final: 0.8753 (mmm) REVERT: D 404 MET cc_start: 0.8426 (tmm) cc_final: 0.8108 (tmm) REVERT: D 408 ILE cc_start: 0.9195 (tp) cc_final: 0.8851 (tp) REVERT: D 412 PHE cc_start: 0.8440 (m-80) cc_final: 0.8223 (m-80) REVERT: A 107 HIS cc_start: 0.8823 (p90) cc_final: 0.7951 (p90) REVERT: A 220 MET cc_start: 0.7406 (pmm) cc_final: 0.7038 (pmm) REVERT: A 263 MET cc_start: 0.8684 (mmm) cc_final: 0.8375 (mmp) REVERT: A 274 LEU cc_start: 0.9511 (mp) cc_final: 0.9142 (tt) REVERT: A 287 MET cc_start: 0.9324 (mmm) cc_final: 0.8615 (mmm) REVERT: A 306 PHE cc_start: 0.8624 (t80) cc_final: 0.8216 (t80) REVERT: A 404 MET cc_start: 0.7946 (tmm) cc_final: 0.7719 (tmm) REVERT: B 17 LEU cc_start: 0.9248 (tp) cc_final: 0.8800 (tp) REVERT: B 97 ASP cc_start: 0.8059 (p0) cc_final: 0.7459 (p0) REVERT: B 110 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7395 (pt0) REVERT: B 142 LEU cc_start: 0.9379 (mp) cc_final: 0.9079 (mp) REVERT: B 186 GLN cc_start: 0.8395 (pm20) cc_final: 0.7976 (pm20) REVERT: B 226 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 235 VAL cc_start: 0.9566 (p) cc_final: 0.8725 (p) REVERT: B 239 TRP cc_start: 0.8304 (m-90) cc_final: 0.6881 (m-90) REVERT: B 242 PHE cc_start: 0.8148 (m-80) cc_final: 0.7816 (m-80) REVERT: B 279 TYR cc_start: 0.7953 (p90) cc_final: 0.7291 (p90) REVERT: C 15 ASP cc_start: 0.8404 (t0) cc_final: 0.8199 (t0) REVERT: C 17 LEU cc_start: 0.9293 (tp) cc_final: 0.8897 (tp) REVERT: C 18 MET cc_start: 0.8757 (pmm) cc_final: 0.8072 (pmm) REVERT: C 97 ASP cc_start: 0.7744 (p0) cc_final: 0.7050 (p0) REVERT: C 102 ASN cc_start: 0.8424 (p0) cc_final: 0.7725 (p0) REVERT: C 167 ILE cc_start: 0.7734 (tt) cc_final: 0.7357 (tt) REVERT: C 404 MET cc_start: 0.8612 (ttt) cc_final: 0.7999 (tpp) REVERT: C 411 MET cc_start: 0.8139 (mtm) cc_final: 0.7396 (mmp) REVERT: E 115 CYS cc_start: 0.8669 (t) cc_final: 0.8423 (t) REVERT: E 122 PHE cc_start: 0.9141 (p90) cc_final: 0.8538 (p90) REVERT: E 170 MET cc_start: 0.8402 (mmm) cc_final: 0.8191 (mmm) REVERT: E 173 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7238 (mm110) REVERT: E 200 GLN cc_start: 0.8677 (mp10) cc_final: 0.8347 (mp-120) REVERT: E 235 GLU cc_start: 0.7678 (tm-30) cc_final: 0.6885 (tm-30) REVERT: E 310 TRP cc_start: 0.9247 (t-100) cc_final: 0.8985 (t-100) REVERT: E 329 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8521 (mm-40) REVERT: E 465 PHE cc_start: 0.8374 (p90) cc_final: 0.7313 (p90) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.0990 time to fit residues: 58.6242 Evaluate side-chains 312 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 56 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 149 optimal weight: 0.0040 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN A 61 ASN A 171 GLN A 186 GLN ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.117513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095761 restraints weight = 36969.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098869 restraints weight = 20148.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100912 restraints weight = 13202.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102308 restraints weight = 9823.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103156 restraints weight = 8001.852| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14163 Z= 0.138 Angle : 0.700 9.319 19179 Z= 0.351 Chirality : 0.047 0.348 2138 Planarity : 0.004 0.042 2386 Dihedral : 7.438 105.637 1981 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.29 (0.21), residues: 1662 helix: 1.78 (0.22), residues: 577 sheet: -0.63 (0.31), residues: 307 loop : -1.58 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.013 0.001 TYR B 301 PHE 0.041 0.002 PHE C 293 TRP 0.013 0.001 TRP B 239 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00321 (14148) covalent geometry : angle 0.69334 (19144) SS BOND : bond 0.00360 ( 10) SS BOND : angle 2.55073 ( 20) hydrogen bonds : bond 0.03995 ( 653) hydrogen bonds : angle 4.64153 ( 1932) link_NAG-ASN : bond 0.00322 ( 5) link_NAG-ASN : angle 1.88640 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.489 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: D 141 ASP cc_start: 0.9101 (t0) cc_final: 0.8691 (t0) REVERT: D 404 MET cc_start: 0.8430 (tmm) cc_final: 0.8096 (tmm) REVERT: D 408 ILE cc_start: 0.9162 (tp) cc_final: 0.8878 (tp) REVERT: D 412 PHE cc_start: 0.8425 (m-80) cc_final: 0.8125 (m-10) REVERT: A 107 HIS cc_start: 0.8711 (p90) cc_final: 0.7928 (p90) REVERT: A 140 MET cc_start: 0.8431 (mmm) cc_final: 0.8116 (mmm) REVERT: A 220 MET cc_start: 0.7377 (pmm) cc_final: 0.6999 (pmm) REVERT: A 274 LEU cc_start: 0.9519 (mp) cc_final: 0.9139 (tt) REVERT: A 287 MET cc_start: 0.9211 (mmm) cc_final: 0.8747 (mmm) REVERT: A 306 PHE cc_start: 0.8641 (t80) cc_final: 0.8240 (t80) REVERT: B 17 LEU cc_start: 0.9269 (tp) cc_final: 0.8983 (tp) REVERT: B 97 ASP cc_start: 0.8039 (p0) cc_final: 0.7432 (p0) REVERT: B 110 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7303 (pt0) REVERT: B 142 LEU cc_start: 0.9373 (mp) cc_final: 0.9048 (mp) REVERT: B 226 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8271 (tm-30) REVERT: B 235 VAL cc_start: 0.9557 (p) cc_final: 0.8550 (p) REVERT: B 239 TRP cc_start: 0.8260 (m-90) cc_final: 0.6827 (m-90) REVERT: B 242 PHE cc_start: 0.8133 (m-80) cc_final: 0.7890 (m-80) REVERT: B 279 TYR cc_start: 0.7931 (p90) cc_final: 0.7227 (p90) REVERT: C 15 ASP cc_start: 0.8460 (t0) cc_final: 0.8216 (t0) REVERT: C 17 LEU cc_start: 0.9268 (tp) cc_final: 0.8887 (tp) REVERT: C 18 MET cc_start: 0.8610 (pmm) cc_final: 0.8051 (pmm) REVERT: C 97 ASP cc_start: 0.7732 (p0) cc_final: 0.7008 (p0) REVERT: C 102 ASN cc_start: 0.8437 (p0) cc_final: 0.7766 (p0) REVERT: C 167 ILE cc_start: 0.7708 (tt) cc_final: 0.7315 (tt) REVERT: C 404 MET cc_start: 0.8624 (ttt) cc_final: 0.8000 (tpp) REVERT: C 411 MET cc_start: 0.8100 (mtm) cc_final: 0.7852 (ttt) REVERT: E 170 MET cc_start: 0.8426 (mmm) cc_final: 0.8176 (mmm) REVERT: E 173 GLN cc_start: 0.7754 (mm-40) cc_final: 0.6813 (mm110) REVERT: E 200 GLN cc_start: 0.8684 (mp10) cc_final: 0.8076 (mp10) REVERT: E 201 LEU cc_start: 0.6531 (tp) cc_final: 0.6324 (tp) REVERT: E 310 TRP cc_start: 0.9297 (t-100) cc_final: 0.9039 (t-100) REVERT: E 324 GLU cc_start: 0.8164 (pp20) cc_final: 0.7833 (mm-30) REVERT: E 329 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8517 (mm-40) REVERT: E 465 PHE cc_start: 0.8343 (p90) cc_final: 0.7261 (p90) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.0968 time to fit residues: 55.6375 Evaluate side-chains 307 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092530 restraints weight = 37289.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095485 restraints weight = 20406.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097413 restraints weight = 13495.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098754 restraints weight = 10157.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099576 restraints weight = 8336.725| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14163 Z= 0.192 Angle : 0.718 9.674 19179 Z= 0.366 Chirality : 0.047 0.330 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.521 106.489 1981 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1662 helix: 1.71 (0.22), residues: 576 sheet: -0.60 (0.31), residues: 308 loop : -1.61 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 29 TYR 0.021 0.001 TYR A 301 PHE 0.041 0.002 PHE D 293 TRP 0.024 0.001 TRP C 170 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00441 (14148) covalent geometry : angle 0.71308 (19144) SS BOND : bond 0.00270 ( 10) SS BOND : angle 2.42996 ( 20) hydrogen bonds : bond 0.04266 ( 653) hydrogen bonds : angle 4.70716 ( 1932) link_NAG-ASN : bond 0.00313 ( 5) link_NAG-ASN : angle 1.76957 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.580 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: D 89 MET cc_start: 0.9488 (mmp) cc_final: 0.9281 (tpp) REVERT: D 141 ASP cc_start: 0.9102 (t0) cc_final: 0.8513 (t0) REVERT: D 287 MET cc_start: 0.9193 (mmm) cc_final: 0.8829 (mmm) REVERT: D 404 MET cc_start: 0.8452 (tmm) cc_final: 0.8105 (tmm) REVERT: D 408 ILE cc_start: 0.9154 (tp) cc_final: 0.8874 (tp) REVERT: D 412 PHE cc_start: 0.8435 (m-80) cc_final: 0.8158 (m-10) REVERT: A 220 MET cc_start: 0.7402 (pmm) cc_final: 0.7053 (pmm) REVERT: A 274 LEU cc_start: 0.9541 (mp) cc_final: 0.9155 (tt) REVERT: A 287 MET cc_start: 0.9288 (mmm) cc_final: 0.8741 (mmm) REVERT: A 404 MET cc_start: 0.8024 (tmm) cc_final: 0.7792 (tmm) REVERT: B 97 ASP cc_start: 0.8098 (p0) cc_final: 0.7480 (p0) REVERT: B 103 GLU cc_start: 0.7866 (pp20) cc_final: 0.7431 (pp20) REVERT: B 110 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7424 (pt0) REVERT: B 142 LEU cc_start: 0.9309 (mp) cc_final: 0.9096 (mp) REVERT: B 226 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8311 (tt0) REVERT: B 235 VAL cc_start: 0.9592 (p) cc_final: 0.8604 (p) REVERT: B 239 TRP cc_start: 0.8330 (m-90) cc_final: 0.6820 (m-90) REVERT: B 242 PHE cc_start: 0.8198 (m-80) cc_final: 0.7909 (m-80) REVERT: C 15 ASP cc_start: 0.8420 (t0) cc_final: 0.8086 (t0) REVERT: C 17 LEU cc_start: 0.9299 (tp) cc_final: 0.8875 (tp) REVERT: C 18 MET cc_start: 0.8675 (pmm) cc_final: 0.8014 (pmm) REVERT: C 97 ASP cc_start: 0.7833 (p0) cc_final: 0.7144 (p0) REVERT: C 102 ASN cc_start: 0.8498 (p0) cc_final: 0.7814 (p0) REVERT: C 167 ILE cc_start: 0.7889 (tt) cc_final: 0.7512 (tt) REVERT: C 404 MET cc_start: 0.8571 (ttt) cc_final: 0.7958 (tpp) REVERT: C 411 MET cc_start: 0.8122 (mtm) cc_final: 0.7912 (ttt) REVERT: E 115 CYS cc_start: 0.8642 (t) cc_final: 0.8381 (t) REVERT: E 170 MET cc_start: 0.8416 (mmm) cc_final: 0.8207 (mmm) REVERT: E 173 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7603 (mm110) REVERT: E 200 GLN cc_start: 0.8721 (mp10) cc_final: 0.8278 (mp10) REVERT: E 201 LEU cc_start: 0.6569 (tp) cc_final: 0.6355 (tp) REVERT: E 235 GLU cc_start: 0.7708 (tm-30) cc_final: 0.6988 (tm-30) REVERT: E 243 GLN cc_start: 0.7860 (pp30) cc_final: 0.7472 (pm20) REVERT: E 310 TRP cc_start: 0.9312 (t-100) cc_final: 0.9062 (t-100) REVERT: E 329 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8547 (mm-40) REVERT: E 465 PHE cc_start: 0.8387 (p90) cc_final: 0.7250 (p90) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.0931 time to fit residues: 53.0190 Evaluate side-chains 302 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 127 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 171 GLN A 186 GLN ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093965 restraints weight = 37147.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.096984 restraints weight = 20409.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099027 restraints weight = 13477.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100376 restraints weight = 10062.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101325 restraints weight = 8245.093| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14163 Z= 0.161 Angle : 0.725 11.835 19179 Z= 0.366 Chirality : 0.047 0.264 2138 Planarity : 0.004 0.042 2386 Dihedral : 7.476 105.197 1981 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.08 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.30 (0.21), residues: 1662 helix: 1.72 (0.22), residues: 576 sheet: -0.52 (0.31), residues: 308 loop : -1.59 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 29 TYR 0.013 0.001 TYR A 301 PHE 0.025 0.002 PHE C 242 TRP 0.012 0.001 TRP A 414 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00372 (14148) covalent geometry : angle 0.71962 (19144) SS BOND : bond 0.00249 ( 10) SS BOND : angle 2.55146 ( 20) hydrogen bonds : bond 0.04133 ( 653) hydrogen bonds : angle 4.64747 ( 1932) link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 1.70155 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.520 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: D 287 MET cc_start: 0.9205 (mmm) cc_final: 0.8830 (mmm) REVERT: D 404 MET cc_start: 0.8445 (tmm) cc_final: 0.8093 (tmm) REVERT: D 408 ILE cc_start: 0.9135 (tp) cc_final: 0.8841 (tp) REVERT: D 412 PHE cc_start: 0.8411 (m-80) cc_final: 0.8115 (m-10) REVERT: A 220 MET cc_start: 0.7395 (pmm) cc_final: 0.7000 (pmm) REVERT: A 274 LEU cc_start: 0.9518 (mp) cc_final: 0.9138 (tt) REVERT: A 287 MET cc_start: 0.9323 (mmm) cc_final: 0.8737 (mmm) REVERT: A 404 MET cc_start: 0.8057 (tmm) cc_final: 0.7843 (tmm) REVERT: B 97 ASP cc_start: 0.8037 (p0) cc_final: 0.7480 (p0) REVERT: B 110 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7307 (pt0) REVERT: B 163 MET cc_start: 0.8136 (mmp) cc_final: 0.7728 (mmp) REVERT: B 226 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8398 (tt0) REVERT: B 239 TRP cc_start: 0.8239 (m-10) cc_final: 0.8031 (m-10) REVERT: B 242 PHE cc_start: 0.8095 (m-80) cc_final: 0.7788 (m-80) REVERT: C 15 ASP cc_start: 0.8419 (t0) cc_final: 0.8089 (t0) REVERT: C 17 LEU cc_start: 0.9282 (tp) cc_final: 0.8872 (tp) REVERT: C 18 MET cc_start: 0.8588 (pmm) cc_final: 0.8070 (pmm) REVERT: C 97 ASP cc_start: 0.7775 (p0) cc_final: 0.7089 (p0) REVERT: C 102 ASN cc_start: 0.8490 (p0) cc_final: 0.7810 (p0) REVERT: C 167 ILE cc_start: 0.7781 (tt) cc_final: 0.7417 (tt) REVERT: C 404 MET cc_start: 0.8636 (ttt) cc_final: 0.8008 (tpp) REVERT: E 77 MET cc_start: 0.8018 (tpp) cc_final: 0.7816 (tpp) REVERT: E 170 MET cc_start: 0.8424 (mmm) cc_final: 0.8192 (mmm) REVERT: E 173 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7119 (mm110) REVERT: E 200 GLN cc_start: 0.8710 (mp10) cc_final: 0.8226 (mp10) REVERT: E 201 LEU cc_start: 0.6476 (tp) cc_final: 0.6269 (tp) REVERT: E 235 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7094 (tm-30) REVERT: E 310 TRP cc_start: 0.9334 (t-100) cc_final: 0.9079 (t-100) REVERT: E 324 GLU cc_start: 0.8184 (pp20) cc_final: 0.7841 (mm-30) REVERT: E 329 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8514 (mm-40) REVERT: E 465 PHE cc_start: 0.8319 (p90) cc_final: 0.7388 (p90) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.0893 time to fit residues: 51.2275 Evaluate side-chains 299 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092762 restraints weight = 37465.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095732 restraints weight = 20626.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097700 restraints weight = 13662.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099017 restraints weight = 10271.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099863 restraints weight = 8449.488| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14163 Z= 0.190 Angle : 0.746 12.344 19179 Z= 0.378 Chirality : 0.048 0.280 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.595 105.453 1981 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.39 (0.21), residues: 1662 helix: 1.67 (0.22), residues: 576 sheet: -0.59 (0.31), residues: 307 loop : -1.66 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 29 TYR 0.012 0.001 TYR A 301 PHE 0.023 0.002 PHE B 412 TRP 0.014 0.001 TRP C 170 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00436 (14148) covalent geometry : angle 0.74149 (19144) SS BOND : bond 0.00257 ( 10) SS BOND : angle 2.40309 ( 20) hydrogen bonds : bond 0.04307 ( 653) hydrogen bonds : angle 4.68096 ( 1932) link_NAG-ASN : bond 0.00310 ( 5) link_NAG-ASN : angle 1.70048 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.573 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: D 242 PHE cc_start: 0.7126 (m-80) cc_final: 0.6892 (m-80) REVERT: D 404 MET cc_start: 0.8438 (tmm) cc_final: 0.8090 (tmm) REVERT: D 408 ILE cc_start: 0.9133 (tp) cc_final: 0.8830 (tp) REVERT: D 412 PHE cc_start: 0.8412 (m-80) cc_final: 0.8114 (m-10) REVERT: A 220 MET cc_start: 0.7430 (pmm) cc_final: 0.6948 (pmm) REVERT: A 274 LEU cc_start: 0.9535 (mp) cc_final: 0.9160 (tt) REVERT: A 287 MET cc_start: 0.9333 (mmm) cc_final: 0.8734 (mmm) REVERT: A 404 MET cc_start: 0.8142 (tmm) cc_final: 0.7914 (tmm) REVERT: B 97 ASP cc_start: 0.8123 (p0) cc_final: 0.7597 (p0) REVERT: B 103 GLU cc_start: 0.7852 (pp20) cc_final: 0.7439 (pp20) REVERT: B 142 LEU cc_start: 0.9135 (mp) cc_final: 0.8851 (mp) REVERT: B 163 MET cc_start: 0.8198 (mmp) cc_final: 0.7797 (mmp) REVERT: B 239 TRP cc_start: 0.8290 (m-10) cc_final: 0.8026 (m-10) REVERT: B 242 PHE cc_start: 0.8174 (m-80) cc_final: 0.7828 (m-80) REVERT: B 265 THR cc_start: 0.8834 (t) cc_final: 0.8634 (m) REVERT: B 279 TYR cc_start: 0.8014 (p90) cc_final: 0.7270 (p90) REVERT: C 15 ASP cc_start: 0.8414 (t0) cc_final: 0.8041 (t0) REVERT: C 97 ASP cc_start: 0.7798 (p0) cc_final: 0.7111 (p0) REVERT: C 102 ASN cc_start: 0.8482 (p0) cc_final: 0.7799 (p0) REVERT: C 404 MET cc_start: 0.8600 (ttt) cc_final: 0.7988 (tpp) REVERT: E 74 GLU cc_start: 0.8289 (mp0) cc_final: 0.8084 (mp0) REVERT: E 115 CYS cc_start: 0.8655 (t) cc_final: 0.8382 (t) REVERT: E 173 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7201 (mm110) REVERT: E 200 GLN cc_start: 0.8754 (mp10) cc_final: 0.8264 (mp10) REVERT: E 235 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7137 (tm-30) REVERT: E 310 TRP cc_start: 0.9328 (t-100) cc_final: 0.9070 (t-100) REVERT: E 324 GLU cc_start: 0.8339 (pp20) cc_final: 0.7914 (mm-30) REVERT: E 329 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8521 (mm-40) REVERT: E 465 PHE cc_start: 0.8358 (p90) cc_final: 0.7384 (p90) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.0930 time to fit residues: 52.6105 Evaluate side-chains 292 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 0.0470 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN D 102 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.118031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096187 restraints weight = 36730.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099287 restraints weight = 20201.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101324 restraints weight = 13310.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102750 restraints weight = 9949.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103606 restraints weight = 8112.540| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14163 Z= 0.138 Angle : 0.746 14.147 19179 Z= 0.369 Chirality : 0.048 0.283 2138 Planarity : 0.004 0.042 2386 Dihedral : 7.422 103.161 1981 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.35 % Favored : 94.46 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1662 helix: 1.71 (0.22), residues: 576 sheet: -0.50 (0.31), residues: 307 loop : -1.65 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.025 0.001 TYR B 301 PHE 0.023 0.002 PHE B 13 TRP 0.013 0.001 TRP A 414 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00315 (14148) covalent geometry : angle 0.74195 (19144) SS BOND : bond 0.00296 ( 10) SS BOND : angle 2.25830 ( 20) hydrogen bonds : bond 0.04028 ( 653) hydrogen bonds : angle 4.58338 ( 1932) link_NAG-ASN : bond 0.00353 ( 5) link_NAG-ASN : angle 1.60260 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (p0) REVERT: D 141 ASP cc_start: 0.9052 (t0) cc_final: 0.8613 (t0) REVERT: D 145 PHE cc_start: 0.8753 (t80) cc_final: 0.8503 (t80) REVERT: D 242 PHE cc_start: 0.7108 (m-80) cc_final: 0.6903 (m-80) REVERT: D 287 MET cc_start: 0.9102 (mmm) cc_final: 0.8627 (mmm) REVERT: D 404 MET cc_start: 0.8405 (tmm) cc_final: 0.8052 (tmm) REVERT: D 408 ILE cc_start: 0.9127 (tp) cc_final: 0.8831 (tp) REVERT: D 412 PHE cc_start: 0.8386 (m-80) cc_final: 0.8108 (m-10) REVERT: A 217 GLU cc_start: 0.8077 (mp0) cc_final: 0.7857 (mp0) REVERT: A 220 MET cc_start: 0.7359 (pmm) cc_final: 0.6847 (pmm) REVERT: A 274 LEU cc_start: 0.9539 (mp) cc_final: 0.9170 (tt) REVERT: A 287 MET cc_start: 0.9363 (mmm) cc_final: 0.8648 (mmm) REVERT: A 404 MET cc_start: 0.8138 (tmm) cc_final: 0.7925 (tmm) REVERT: B 97 ASP cc_start: 0.7997 (p0) cc_final: 0.7479 (p0) REVERT: B 110 GLU cc_start: 0.8144 (pt0) cc_final: 0.7910 (pt0) REVERT: B 191 GLU cc_start: 0.8162 (pp20) cc_final: 0.7828 (tm-30) REVERT: B 211 GLU cc_start: 0.7402 (mp0) cc_final: 0.7162 (mp0) REVERT: B 239 TRP cc_start: 0.8264 (m-10) cc_final: 0.8013 (m-10) REVERT: B 242 PHE cc_start: 0.8151 (m-80) cc_final: 0.7838 (m-80) REVERT: C 15 ASP cc_start: 0.8482 (t0) cc_final: 0.8241 (t0) REVERT: C 97 ASP cc_start: 0.7618 (p0) cc_final: 0.6943 (p0) REVERT: C 102 ASN cc_start: 0.8507 (p0) cc_final: 0.7817 (p0) REVERT: C 103 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 404 MET cc_start: 0.8545 (ttt) cc_final: 0.7961 (tpp) REVERT: C 414 TRP cc_start: 0.8967 (m100) cc_final: 0.8698 (m100) REVERT: E 74 GLU cc_start: 0.8297 (mp0) cc_final: 0.8064 (mp0) REVERT: E 173 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7151 (mm110) REVERT: E 200 GLN cc_start: 0.8631 (mp10) cc_final: 0.8207 (mp-120) REVERT: E 235 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7066 (tm-30) REVERT: E 244 VAL cc_start: 0.8353 (t) cc_final: 0.7798 (t) REVERT: E 310 TRP cc_start: 0.9325 (t-100) cc_final: 0.9109 (t-100) REVERT: E 324 GLU cc_start: 0.8291 (pp20) cc_final: 0.7882 (mm-30) REVERT: E 329 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8507 (mm-40) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.0924 time to fit residues: 53.2948 Evaluate side-chains 306 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 77 optimal weight: 0.0070 chunk 137 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.118232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096353 restraints weight = 37129.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099456 restraints weight = 20278.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101562 restraints weight = 13324.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102984 restraints weight = 9896.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103803 restraints weight = 8061.325| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14163 Z= 0.139 Angle : 0.730 10.755 19179 Z= 0.364 Chirality : 0.047 0.273 2138 Planarity : 0.004 0.042 2386 Dihedral : 7.309 102.181 1981 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Rotamer: Outliers : 0.07 % Allowed : 0.46 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.37 (0.21), residues: 1662 helix: 1.66 (0.22), residues: 574 sheet: -0.47 (0.31), residues: 307 loop : -1.66 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.016 0.001 TYR C 413 PHE 0.026 0.002 PHE C 242 TRP 0.012 0.001 TRP C 170 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00322 (14148) covalent geometry : angle 0.72574 (19144) SS BOND : bond 0.00290 ( 10) SS BOND : angle 2.25436 ( 20) hydrogen bonds : bond 0.03923 ( 653) hydrogen bonds : angle 4.53934 ( 1932) link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 1.57132 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.97 seconds wall clock time: 40 minutes 41.72 seconds (2441.72 seconds total)