Starting phenix.real_space_refine on Thu Jun 12 20:16:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn4_27554/06_2025/8dn4_27554_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn4_27554/06_2025/8dn4_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_27554/06_2025/8dn4_27554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn4_27554/06_2025/8dn4_27554.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn4_27554/06_2025/8dn4_27554_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn4_27554/06_2025/8dn4_27554_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'ARG: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: 8.69, per 1000 atoms: 0.63 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: 4.03 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.77 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: 4.27 Time building geometry restraints manager: 4.64 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 419 or resid 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 419 or resid 501)) selection = (chain 'C' and (resid 8 through 309 or resid 387 through 419 or resid 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 419 or resid 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.020 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- 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 : 18.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 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 TRP 0.075 0.002 TRP B 239 HIS 0.001 0.001 HIS D 201 PHE 0.035 0.002 PHE D 412 TYR 0.021 0.001 TYR D 413 ARG 0.008 0.000 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 5) link_NAG-ASN : angle 2.78166 ( 15) hydrogen bonds : bond 0.18017 ( 653) hydrogen bonds : angle 6.73904 ( 1932) SS BOND : bond 0.00287 ( 10) SS BOND : angle 2.51791 ( 20) covalent geometry : bond 0.00360 (14148) covalent geometry : angle 0.72294 (19144) *********************** 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 : 1.611 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: 0.7889 (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: 0.8079 (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: 0.2233 time to fit residues: 144.2153 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 : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN D 150 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093512 restraints weight = 37105.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096493 restraints weight = 20204.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098485 restraints weight = 13271.033| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1440 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= 0.173 Angle : 0.704 10.386 19179 Z= 0.360 Chirality : 0.047 0.323 2138 Planarity : 0.005 0.071 2386 Dihedral : 9.392 111.436 1981 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1662 helix: 1.75 (0.22), residues: 575 sheet: -0.80 (0.30), residues: 311 loop : -1.58 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 239 HIS 0.005 0.001 HIS C 201 PHE 0.026 0.002 PHE A 242 TYR 0.012 0.001 TYR D 413 ARG 0.009 0.001 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 5) link_NAG-ASN : angle 2.48523 ( 15) hydrogen bonds : bond 0.04540 ( 653) hydrogen bonds : angle 5.18622 ( 1932) SS BOND : bond 0.00457 ( 10) SS BOND : angle 2.35429 ( 20) covalent geometry : bond 0.00386 (14148) covalent geometry : angle 0.69705 (19144) *********************** 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 379 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 376 time to evaluate : 1.685 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 17 LEU cc_start: 0.9308 (tp) cc_final: 0.8654 (tp) REVERT: D 18 MET cc_start: 0.9159 (pmm) cc_final: 0.8846 (pmm) REVERT: D 89 MET cc_start: 0.9403 (mmm) cc_final: 0.9074 (mpp) REVERT: D 404 MET cc_start: 0.8560 (tmm) cc_final: 0.8262 (tmm) REVERT: D 408 ILE cc_start: 0.9296 (tp) cc_final: 0.8976 (tp) REVERT: D 412 PHE cc_start: 0.8532 (m-80) cc_final: 0.8103 (m-10) REVERT: A 107 HIS cc_start: 0.8549 (p90) cc_final: 0.8061 (p90) REVERT: A 155 GLN cc_start: 0.8405 (mt0) cc_final: 0.7954 (mt0) REVERT: A 211 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 263 MET cc_start: 0.8733 (mmm) cc_final: 0.8519 (mmp) REVERT: A 274 LEU cc_start: 0.9529 (mp) cc_final: 0.9155 (tt) REVERT: A 287 MET cc_start: 0.9216 (mmm) cc_final: 0.8580 (mmm) REVERT: B 17 LEU cc_start: 0.9333 (tp) cc_final: 0.8833 (tp) REVERT: B 66 GLN cc_start: 0.9054 (mp-120) cc_final: 0.8841 (mp10) REVERT: B 103 GLU cc_start: 0.7819 (pp20) cc_final: 0.7484 (pp20) REVERT: B 173 GLN cc_start: 0.8983 (mp10) cc_final: 0.8576 (mp10) REVERT: B 210 ILE cc_start: 0.9427 (pt) cc_final: 0.9154 (pt) REVERT: B 211 GLU cc_start: 0.7524 (pm20) cc_final: 0.6641 (pm20) REVERT: B 235 VAL cc_start: 0.9595 (p) cc_final: 0.8808 (p) REVERT: B 239 TRP cc_start: 0.8322 (m-90) cc_final: 0.6999 (m-90) REVERT: C 17 LEU cc_start: 0.9299 (tp) cc_final: 0.9027 (tp) REVERT: C 18 MET cc_start: 0.8709 (pmm) cc_final: 0.8135 (pmm) REVERT: C 97 ASP cc_start: 0.7595 (p0) cc_final: 0.6950 (p0) REVERT: C 98 LEU cc_start: 0.9042 (tp) cc_final: 0.8820 (tp) REVERT: C 153 ILE cc_start: 0.9005 (pt) cc_final: 0.8701 (pt) REVERT: C 167 ILE cc_start: 0.7733 (tt) cc_final: 0.7315 (tt) REVERT: C 239 TRP cc_start: 0.7710 (m-10) cc_final: 0.7330 (m-10) REVERT: C 404 MET cc_start: 0.8705 (ttt) cc_final: 0.8319 (tpp) REVERT: C 411 MET cc_start: 0.6891 (tpt) cc_final: 0.6571 (mmp) REVERT: C 414 TRP cc_start: 0.8935 (m100) cc_final: 0.8439 (m100) REVERT: E 74 GLU cc_start: 0.8538 (mp0) cc_final: 0.8190 (mp0) REVERT: E 115 CYS cc_start: 0.8808 (t) cc_final: 0.8580 (t) REVERT: E 125 ASN cc_start: 0.8588 (m110) cc_final: 0.8259 (m110) REVERT: E 155 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9029 (pp) REVERT: E 170 MET cc_start: 0.8289 (mmm) cc_final: 0.7993 (mmm) REVERT: E 173 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7003 (mm110) REVERT: E 176 LYS cc_start: 0.9056 (ptmm) cc_final: 0.8448 (pttt) REVERT: E 314 CYS cc_start: 0.9372 (m) cc_final: 0.9062 (m) outliers start: 3 outliers final: 0 residues processed: 378 average time/residue: 0.2184 time to fit residues: 127.0946 Evaluate side-chains 313 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 150 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS ** 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 63 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.114085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092337 restraints weight = 37067.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095299 restraints weight = 20284.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097273 restraints weight = 13339.512| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14163 Z= 0.199 Angle : 0.703 11.415 19179 Z= 0.359 Chirality : 0.047 0.303 2138 Planarity : 0.005 0.058 2386 Dihedral : 8.346 109.744 1981 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 0.13 % Allowed : 4.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1662 helix: 1.72 (0.22), residues: 576 sheet: -0.87 (0.30), residues: 312 loop : -1.69 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 414 HIS 0.006 0.001 HIS C 201 PHE 0.049 0.002 PHE B 242 TYR 0.014 0.001 TYR E 224 ARG 0.007 0.000 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 2.35209 ( 15) hydrogen bonds : bond 0.04502 ( 653) hydrogen bonds : angle 4.93279 ( 1932) SS BOND : bond 0.00602 ( 10) SS BOND : angle 1.68707 ( 20) covalent geometry : bond 0.00451 (14148) covalent geometry : angle 0.69810 (19144) *********************** 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 385 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 383 time to evaluate : 1.727 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: 0.9145 (t0) cc_final: 0.8787 (t0) REVERT: D 145 PHE cc_start: 0.9287 (t80) cc_final: 0.9048 (t80) REVERT: D 311 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6323 (m-70) REVERT: D 404 MET cc_start: 0.8470 (tmm) cc_final: 0.8158 (tmm) REVERT: D 408 ILE cc_start: 0.9272 (tp) cc_final: 0.8997 (tp) REVERT: D 412 PHE cc_start: 0.8531 (m-80) cc_final: 0.8158 (m-10) REVERT: A 107 HIS cc_start: 0.8797 (p90) cc_final: 0.8075 (p90) REVERT: A 220 MET cc_start: 0.7457 (pmm) cc_final: 0.7215 (pmm) REVERT: A 246 MET cc_start: 0.9354 (ppp) cc_final: 0.8800 (ppp) REVERT: A 274 LEU cc_start: 0.9519 (mp) cc_final: 0.9150 (tt) REVERT: A 287 MET cc_start: 0.9246 (mmm) cc_final: 0.8563 (mmm) REVERT: B 17 LEU cc_start: 0.9341 (tp) cc_final: 0.8963 (tp) REVERT: B 97 ASP cc_start: 0.8173 (p0) cc_final: 0.7669 (p0) REVERT: B 103 GLU cc_start: 0.7914 (pp20) cc_final: 0.7514 (pp20) REVERT: B 211 GLU cc_start: 0.7123 (pm20) cc_final: 0.6913 (pm20) REVERT: B 220 MET cc_start: 0.7853 (pmm) cc_final: 0.7523 (pmm) REVERT: B 226 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 242 PHE cc_start: 0.8041 (m-80) cc_final: 0.7788 (m-80) REVERT: C 17 LEU cc_start: 0.9306 (tp) cc_final: 0.8916 (tp) REVERT: C 18 MET cc_start: 0.8654 (pmm) cc_final: 0.8009 (pmm) REVERT: C 97 ASP cc_start: 0.7814 (p0) cc_final: 0.7149 (p0) REVERT: C 167 ILE cc_start: 0.7818 (tt) cc_final: 0.7405 (tt) REVERT: C 238 SER cc_start: 0.8243 (p) cc_final: 0.7978 (p) REVERT: C 239 TRP cc_start: 0.7667 (m-10) cc_final: 0.6824 (m-10) REVERT: C 283 ILE cc_start: 0.8095 (tt) cc_final: 0.7559 (tt) REVERT: C 404 MET cc_start: 0.8690 (ttt) cc_final: 0.8091 (tpp) REVERT: C 411 MET cc_start: 0.6573 (tpt) cc_final: 0.6245 (mmp) REVERT: C 414 TRP cc_start: 0.8956 (m100) cc_final: 0.8461 (m100) REVERT: E 77 MET cc_start: 0.8334 (tpp) cc_final: 0.8083 (tpp) REVERT: E 115 CYS cc_start: 0.8792 (t) cc_final: 0.8574 (t) REVERT: E 125 ASN cc_start: 0.8629 (m110) cc_final: 0.8239 (m110) REVERT: E 173 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7414 (mm110) REVERT: E 176 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8393 (pttt) REVERT: E 200 GLN cc_start: 0.8719 (mp10) cc_final: 0.8392 (mp-120) REVERT: E 314 CYS cc_start: 0.9413 (m) cc_final: 0.9118 (m) REVERT: E 465 PHE cc_start: 0.8269 (p90) cc_final: 0.8003 (p90) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.2227 time to fit residues: 129.7513 Evaluate side-chains 301 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN 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** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN E 329 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093927 restraints weight = 36711.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096889 restraints weight = 19951.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098850 restraints weight = 13129.801| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14163 Z= 0.150 Angle : 0.679 10.063 19179 Z= 0.342 Chirality : 0.046 0.303 2138 Planarity : 0.004 0.050 2386 Dihedral : 7.780 108.003 1981 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1662 helix: 1.72 (0.22), residues: 576 sheet: -0.83 (0.30), residues: 322 loop : -1.60 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 239 HIS 0.007 0.001 HIS C 201 PHE 0.034 0.002 PHE E 282 TYR 0.013 0.001 TYR B 301 ARG 0.006 0.000 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 2.53241 ( 15) hydrogen bonds : bond 0.04188 ( 653) hydrogen bonds : angle 4.74577 ( 1932) SS BOND : bond 0.00256 ( 10) SS BOND : angle 1.79980 ( 20) covalent geometry : bond 0.00342 (14148) covalent geometry : angle 0.67296 (19144) *********************** 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 380 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.578 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 89 MET cc_start: 0.9463 (mmt) cc_final: 0.9237 (mpp) REVERT: D 141 ASP cc_start: 0.9134 (t0) cc_final: 0.8885 (t0) REVERT: D 148 ASP cc_start: 0.8753 (t0) cc_final: 0.8240 (t0) REVERT: D 226 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8836 (tm-30) REVERT: D 404 MET cc_start: 0.8487 (tmm) cc_final: 0.8153 (tmm) REVERT: D 408 ILE cc_start: 0.9222 (tp) cc_final: 0.8912 (tp) REVERT: D 412 PHE cc_start: 0.8499 (m-80) cc_final: 0.8264 (m-80) REVERT: A 107 HIS cc_start: 0.8836 (p90) cc_final: 0.8014 (p90) REVERT: A 220 MET cc_start: 0.7423 (pmm) cc_final: 0.7076 (pmm) REVERT: A 262 THR cc_start: 0.9529 (p) cc_final: 0.8941 (p) REVERT: A 263 MET cc_start: 0.8795 (mmm) cc_final: 0.8491 (mmp) REVERT: A 274 LEU cc_start: 0.9506 (mp) cc_final: 0.9145 (tt) REVERT: A 287 MET cc_start: 0.9285 (mmm) cc_final: 0.8622 (mmm) REVERT: A 306 PHE cc_start: 0.8655 (t80) cc_final: 0.8273 (t80) REVERT: B 97 ASP cc_start: 0.8169 (p0) cc_final: 0.7549 (p0) REVERT: B 110 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7341 (pt0) REVERT: B 157 GLU cc_start: 0.8295 (pt0) cc_final: 0.7677 (pt0) REVERT: B 192 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 220 MET cc_start: 0.7814 (pmm) cc_final: 0.7514 (pmm) REVERT: B 226 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 239 TRP cc_start: 0.8294 (m-90) cc_final: 0.6944 (m-90) REVERT: B 242 PHE cc_start: 0.8140 (m-80) cc_final: 0.7795 (m-80) REVERT: B 279 TYR cc_start: 0.8009 (p90) cc_final: 0.7400 (p90) REVERT: C 17 LEU cc_start: 0.9291 (tp) cc_final: 0.8898 (tp) REVERT: C 18 MET cc_start: 0.8704 (pmm) cc_final: 0.8034 (pmm) REVERT: C 97 ASP cc_start: 0.7792 (p0) cc_final: 0.7094 (p0) REVERT: C 102 ASN cc_start: 0.8362 (p0) cc_final: 0.7753 (p0) REVERT: C 103 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 404 MET cc_start: 0.8733 (ttt) cc_final: 0.8141 (tpp) REVERT: C 411 MET cc_start: 0.6494 (tpt) cc_final: 0.6157 (mmp) REVERT: C 414 TRP cc_start: 0.8891 (m100) cc_final: 0.8387 (m100) REVERT: E 74 GLU cc_start: 0.8432 (mp0) cc_final: 0.8216 (mp0) REVERT: E 77 MET cc_start: 0.8294 (tpp) cc_final: 0.8018 (tpp) REVERT: E 115 CYS cc_start: 0.8703 (t) cc_final: 0.8466 (t) REVERT: E 170 MET cc_start: 0.8398 (mmm) cc_final: 0.8040 (mmm) REVERT: E 176 LYS cc_start: 0.9075 (ptmm) cc_final: 0.8378 (pttt) REVERT: E 200 GLN cc_start: 0.8687 (mp10) cc_final: 0.8062 (mp10) REVERT: E 235 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6798 (tm-30) REVERT: E 310 TRP cc_start: 0.9295 (t-100) cc_final: 0.8987 (t-100) REVERT: E 314 CYS cc_start: 0.9310 (m) cc_final: 0.8844 (m) REVERT: E 465 PHE cc_start: 0.8300 (p90) cc_final: 0.7131 (p90) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.2221 time to fit residues: 128.6062 Evaluate side-chains 318 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 69 optimal weight: 0.0670 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN D 155 GLN D 177 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** E 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096319 restraints weight = 36751.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099413 restraints weight = 20051.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101479 restraints weight = 13162.530| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2276 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= 0.132 Angle : 0.682 10.261 19179 Z= 0.343 Chirality : 0.046 0.317 2138 Planarity : 0.004 0.046 2386 Dihedral : 7.718 106.164 1981 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1662 helix: 1.76 (0.22), residues: 577 sheet: -0.57 (0.31), residues: 307 loop : -1.58 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 239 HIS 0.006 0.001 HIS C 201 PHE 0.035 0.002 PHE C 293 TYR 0.023 0.001 TYR A 301 ARG 0.008 0.000 ARG A 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 5) link_NAG-ASN : angle 2.29843 ( 15) hydrogen bonds : bond 0.03957 ( 653) hydrogen bonds : angle 4.62721 ( 1932) SS BOND : bond 0.00339 ( 10) SS BOND : angle 2.65021 ( 20) covalent geometry : bond 0.00300 (14148) covalent geometry : angle 0.67456 (19144) *********************** 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 383 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9021 (t0) cc_final: 0.8808 (t0) REVERT: D 287 MET cc_start: 0.9171 (mmm) cc_final: 0.8687 (mmm) REVERT: D 404 MET cc_start: 0.8490 (tmm) cc_final: 0.8136 (tmm) REVERT: D 408 ILE cc_start: 0.9205 (tp) cc_final: 0.8882 (tp) REVERT: D 412 PHE cc_start: 0.8454 (m-80) cc_final: 0.8248 (m-80) REVERT: A 107 HIS cc_start: 0.8671 (p90) cc_final: 0.7913 (p90) REVERT: A 140 MET cc_start: 0.8522 (mmm) cc_final: 0.8247 (mmm) REVERT: A 220 MET cc_start: 0.7328 (pmm) cc_final: 0.6955 (pmm) REVERT: A 263 MET cc_start: 0.8721 (mmm) cc_final: 0.8283 (mmp) REVERT: A 274 LEU cc_start: 0.9486 (mp) cc_final: 0.9129 (tt) REVERT: A 287 MET cc_start: 0.9268 (mmm) cc_final: 0.8629 (mmm) REVERT: A 306 PHE cc_start: 0.8674 (t80) cc_final: 0.8278 (t80) REVERT: A 404 MET cc_start: 0.7943 (tmm) cc_final: 0.7722 (tmm) REVERT: B 97 ASP cc_start: 0.8126 (p0) cc_final: 0.7504 (p0) REVERT: B 226 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 239 TRP cc_start: 0.8229 (m-90) cc_final: 0.7902 (m100) REVERT: B 242 PHE cc_start: 0.8101 (m-80) cc_final: 0.7252 (m-80) REVERT: B 279 TYR cc_start: 0.7986 (p90) cc_final: 0.7373 (p90) REVERT: C 17 LEU cc_start: 0.9300 (tp) cc_final: 0.8904 (tp) REVERT: C 18 MET cc_start: 0.8660 (pmm) cc_final: 0.7993 (pmm) REVERT: C 97 ASP cc_start: 0.7737 (p0) cc_final: 0.7015 (p0) REVERT: C 102 ASN cc_start: 0.8388 (p0) cc_final: 0.7720 (p0) REVERT: C 167 ILE cc_start: 0.7670 (tt) cc_final: 0.7296 (tt) REVERT: C 404 MET cc_start: 0.8666 (ttt) cc_final: 0.8049 (tpp) REVERT: C 411 MET cc_start: 0.6484 (tpt) cc_final: 0.6029 (mmp) REVERT: E 74 GLU cc_start: 0.8292 (mp0) cc_final: 0.8043 (mp0) REVERT: E 77 MET cc_start: 0.8124 (tpp) cc_final: 0.7923 (tpp) REVERT: E 115 CYS cc_start: 0.8668 (t) cc_final: 0.8426 (t) REVERT: E 170 MET cc_start: 0.8339 (mmm) cc_final: 0.8067 (mmm) REVERT: E 200 GLN cc_start: 0.8681 (mp10) cc_final: 0.8307 (mp-120) REVERT: E 201 LEU cc_start: 0.6755 (tp) cc_final: 0.6503 (tp) REVERT: E 235 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6916 (tm-30) REVERT: E 310 TRP cc_start: 0.9249 (t-100) cc_final: 0.8975 (t-100) REVERT: E 324 GLU cc_start: 0.8135 (pp20) cc_final: 0.7825 (mm-30) REVERT: E 329 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8486 (mm-40) REVERT: E 465 PHE cc_start: 0.8324 (p90) cc_final: 0.7317 (p90) outliers start: 1 outliers final: 0 residues processed: 382 average time/residue: 0.2213 time to fit residues: 128.2321 Evaluate side-chains 305 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN A 61 ASN A 171 GLN A 177 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** E 138 ASN E 173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092039 restraints weight = 37742.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095026 restraints weight = 20553.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096961 restraints weight = 13547.888| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14163 Z= 0.181 Angle : 0.705 9.774 19179 Z= 0.358 Chirality : 0.047 0.335 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.578 106.280 1981 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1662 helix: 1.75 (0.22), residues: 576 sheet: -0.61 (0.31), residues: 308 loop : -1.62 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 170 HIS 0.006 0.001 HIS C 201 PHE 0.029 0.002 PHE E 282 TYR 0.024 0.001 TYR A 301 ARG 0.007 0.001 ARG B 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 1.97804 ( 15) hydrogen bonds : bond 0.04148 ( 653) hydrogen bonds : angle 4.68300 ( 1932) SS BOND : bond 0.00485 ( 10) SS BOND : angle 2.64913 ( 20) covalent geometry : bond 0.00415 (14148) covalent geometry : angle 0.69784 (19144) *********************** 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 374 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.497 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 141 ASP cc_start: 0.9163 (t0) cc_final: 0.8883 (t0) REVERT: D 193 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8637 (ptmt) REVERT: D 404 MET cc_start: 0.8517 (tmm) cc_final: 0.8177 (tmm) REVERT: D 408 ILE cc_start: 0.9183 (tp) cc_final: 0.8900 (tp) REVERT: D 412 PHE cc_start: 0.8467 (m-80) cc_final: 0.8153 (m-10) REVERT: A 107 HIS cc_start: 0.8865 (p90) cc_final: 0.7964 (p90) REVERT: A 220 MET cc_start: 0.7348 (pmm) cc_final: 0.7048 (pmm) REVERT: A 263 MET cc_start: 0.8567 (mmm) cc_final: 0.8153 (mmm) REVERT: A 274 LEU cc_start: 0.9529 (mp) cc_final: 0.9146 (tt) REVERT: A 287 MET cc_start: 0.9278 (mmm) cc_final: 0.8749 (mmm) REVERT: B 17 LEU cc_start: 0.9325 (tp) cc_final: 0.9040 (tp) REVERT: B 97 ASP cc_start: 0.8237 (p0) cc_final: 0.7655 (p0) REVERT: B 103 GLU cc_start: 0.7859 (pp20) cc_final: 0.7447 (pp20) REVERT: B 110 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7426 (pt0) REVERT: B 219 GLN cc_start: 0.8749 (pm20) cc_final: 0.8518 (pm20) REVERT: B 220 MET cc_start: 0.7829 (pmm) cc_final: 0.7463 (pmm) REVERT: B 239 TRP cc_start: 0.8291 (m-90) cc_final: 0.6849 (m-90) REVERT: B 242 PHE cc_start: 0.8119 (m-80) cc_final: 0.7861 (m-80) REVERT: B 279 TYR cc_start: 0.8012 (p90) cc_final: 0.7352 (p90) REVERT: C 17 LEU cc_start: 0.9293 (tp) cc_final: 0.8920 (tp) REVERT: C 18 MET cc_start: 0.8564 (pmm) cc_final: 0.8004 (pmm) REVERT: C 97 ASP cc_start: 0.7841 (p0) cc_final: 0.7159 (p0) REVERT: C 102 ASN cc_start: 0.8416 (p0) cc_final: 0.7761 (p0) REVERT: C 103 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7702 (tm-30) REVERT: C 163 MET cc_start: 0.8545 (ptm) cc_final: 0.8344 (ptm) REVERT: C 167 ILE cc_start: 0.7870 (tt) cc_final: 0.7473 (tt) REVERT: C 404 MET cc_start: 0.8701 (ttt) cc_final: 0.8090 (tpp) REVERT: C 411 MET cc_start: 0.6468 (tpt) cc_final: 0.5956 (mmp) REVERT: C 414 TRP cc_start: 0.8885 (m100) cc_final: 0.8316 (m100) REVERT: E 77 MET cc_start: 0.8181 (tpp) cc_final: 0.7899 (tpp) REVERT: E 115 CYS cc_start: 0.8681 (t) cc_final: 0.8409 (t) REVERT: E 200 GLN cc_start: 0.8711 (mp10) cc_final: 0.8367 (mp-120) REVERT: E 201 LEU cc_start: 0.6842 (tp) cc_final: 0.6539 (tp) REVERT: E 235 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6862 (tm-30) REVERT: E 310 TRP cc_start: 0.9206 (t-100) cc_final: 0.8964 (t-100) REVERT: E 329 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8561 (mm-40) REVERT: E 465 PHE cc_start: 0.8365 (p90) cc_final: 0.7315 (p90) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2272 time to fit residues: 128.3295 Evaluate side-chains 294 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 108 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN A 61 ASN A 171 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 = 0.3716 r_free = 0.3716 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095215 restraints weight = 37456.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098333 restraints weight = 20419.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100400 restraints weight = 13380.421| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14163 Z= 0.139 Angle : 0.693 9.284 19179 Z= 0.349 Chirality : 0.046 0.258 2138 Planarity : 0.004 0.045 2386 Dihedral : 7.373 104.821 1981 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1662 helix: 1.77 (0.22), residues: 576 sheet: -0.48 (0.31), residues: 307 loop : -1.60 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.005 0.001 HIS C 201 PHE 0.040 0.002 PHE D 293 TYR 0.015 0.001 TYR B 301 ARG 0.005 0.000 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 5) link_NAG-ASN : angle 1.73563 ( 15) hydrogen bonds : bond 0.03937 ( 653) hydrogen bonds : angle 4.58715 ( 1932) SS BOND : bond 0.00276 ( 10) SS BOND : angle 2.34228 ( 20) covalent geometry : bond 0.00319 (14148) covalent geometry : angle 0.68782 (19144) *********************** 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 369 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.642 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: 0.9120 (t0) cc_final: 0.8700 (t0) REVERT: D 287 MET cc_start: 0.9201 (mmm) cc_final: 0.8852 (mmm) REVERT: D 404 MET cc_start: 0.8494 (tmm) cc_final: 0.8143 (tmm) REVERT: D 408 ILE cc_start: 0.9168 (tp) cc_final: 0.8888 (tp) REVERT: D 412 PHE cc_start: 0.8456 (m-80) cc_final: 0.8176 (m-10) REVERT: A 220 MET cc_start: 0.7307 (pmm) cc_final: 0.6894 (pmm) REVERT: A 274 LEU cc_start: 0.9536 (mp) cc_final: 0.9136 (tt) REVERT: A 287 MET cc_start: 0.9243 (mmm) cc_final: 0.8738 (mmm) REVERT: A 404 MET cc_start: 0.7990 (tmm) cc_final: 0.7787 (tmm) REVERT: B 97 ASP cc_start: 0.8184 (p0) cc_final: 0.7610 (p0) REVERT: B 110 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7400 (pt0) REVERT: B 219 GLN cc_start: 0.8683 (pm20) cc_final: 0.8445 (pm20) REVERT: B 226 GLN cc_start: 0.8832 (tp40) cc_final: 0.8610 (tm-30) REVERT: B 239 TRP cc_start: 0.8267 (m-90) cc_final: 0.6750 (m-90) REVERT: B 242 PHE cc_start: 0.8187 (m-80) cc_final: 0.7912 (m-80) REVERT: B 279 TYR cc_start: 0.8019 (p90) cc_final: 0.7342 (p90) REVERT: C 17 LEU cc_start: 0.9279 (tp) cc_final: 0.8904 (tp) REVERT: C 18 MET cc_start: 0.8572 (pmm) cc_final: 0.8013 (pmm) REVERT: C 97 ASP cc_start: 0.7771 (p0) cc_final: 0.7060 (p0) REVERT: C 102 ASN cc_start: 0.8430 (p0) cc_final: 0.7717 (p0) REVERT: C 103 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 163 MET cc_start: 0.8543 (ptm) cc_final: 0.8319 (ptm) REVERT: C 167 ILE cc_start: 0.7739 (tt) cc_final: 0.7345 (tt) REVERT: C 404 MET cc_start: 0.8661 (ttt) cc_final: 0.8057 (tpp) REVERT: C 411 MET cc_start: 0.6387 (tpt) cc_final: 0.5862 (mmp) REVERT: E 77 MET cc_start: 0.8203 (tpp) cc_final: 0.7891 (tpp) REVERT: E 170 MET cc_start: 0.8409 (mmm) cc_final: 0.8141 (mmm) REVERT: E 200 GLN cc_start: 0.8732 (mp10) cc_final: 0.8409 (mp-120) REVERT: E 201 LEU cc_start: 0.6686 (tp) cc_final: 0.6407 (tp) REVERT: E 235 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7020 (tm-30) REVERT: E 310 TRP cc_start: 0.9274 (t-100) cc_final: 0.9026 (t-100) REVERT: E 324 GLU cc_start: 0.8199 (pp20) cc_final: 0.7880 (mm-30) REVERT: E 329 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8532 (mm-40) REVERT: E 465 PHE cc_start: 0.8404 (p90) cc_final: 0.7335 (p90) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2156 time to fit residues: 121.9996 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 : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** D 177 GLN A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** 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** E 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094861 restraints weight = 37461.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097904 restraints weight = 20577.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099959 restraints weight = 13564.529| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2694 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= 0.160 Angle : 0.724 10.221 19179 Z= 0.365 Chirality : 0.047 0.264 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.384 104.430 1981 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.20 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1662 helix: 1.75 (0.22), residues: 576 sheet: -0.42 (0.31), residues: 307 loop : -1.60 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 170 HIS 0.005 0.001 HIS C 201 PHE 0.025 0.002 PHE C 242 TYR 0.035 0.001 TYR A 301 ARG 0.008 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 1.69911 ( 15) hydrogen bonds : bond 0.04035 ( 653) hydrogen bonds : angle 4.59397 ( 1932) SS BOND : bond 0.00381 ( 10) SS BOND : angle 2.64847 ( 20) covalent geometry : bond 0.00373 (14148) covalent geometry : angle 0.71788 (19144) *********************** 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 362 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 CYS cc_start: 0.6725 (t) cc_final: 0.6016 (t) REVERT: D 141 ASP cc_start: 0.9111 (t0) cc_final: 0.8707 (t0) REVERT: D 287 MET cc_start: 0.9184 (mmm) cc_final: 0.8802 (mmm) REVERT: D 404 MET cc_start: 0.8487 (tmm) cc_final: 0.8135 (tmm) REVERT: D 408 ILE cc_start: 0.9160 (tp) cc_final: 0.8874 (tp) REVERT: D 412 PHE cc_start: 0.8442 (m-80) cc_final: 0.8151 (m-10) REVERT: A 107 HIS cc_start: 0.8712 (p90) cc_final: 0.7899 (p90) REVERT: A 220 MET cc_start: 0.7315 (pmm) cc_final: 0.6862 (pmm) REVERT: A 274 LEU cc_start: 0.9525 (mp) cc_final: 0.9138 (tt) REVERT: A 287 MET cc_start: 0.9288 (mmm) cc_final: 0.8714 (mmm) REVERT: A 404 MET cc_start: 0.8043 (tmm) cc_final: 0.7840 (tmm) REVERT: B 56 MET cc_start: 0.8837 (mmp) cc_final: 0.8626 (mmp) REVERT: B 57 ASP cc_start: 0.8273 (p0) cc_final: 0.8034 (p0) REVERT: B 97 ASP cc_start: 0.8220 (p0) cc_final: 0.7657 (p0) REVERT: B 110 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7410 (pt0) REVERT: B 226 GLN cc_start: 0.8808 (tp40) cc_final: 0.8592 (tm-30) REVERT: B 239 TRP cc_start: 0.8250 (m-10) cc_final: 0.6723 (m-90) REVERT: B 242 PHE cc_start: 0.8170 (m-80) cc_final: 0.7926 (m-80) REVERT: B 279 TYR cc_start: 0.8027 (p90) cc_final: 0.7372 (p90) REVERT: C 17 LEU cc_start: 0.9295 (tp) cc_final: 0.8927 (tp) REVERT: C 18 MET cc_start: 0.8569 (pmm) cc_final: 0.7998 (pmm) REVERT: C 97 ASP cc_start: 0.7780 (p0) cc_final: 0.7079 (p0) REVERT: C 102 ASN cc_start: 0.8407 (p0) cc_final: 0.7718 (p0) REVERT: C 103 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 163 MET cc_start: 0.8527 (ptm) cc_final: 0.8275 (ptm) REVERT: C 167 ILE cc_start: 0.7796 (tt) cc_final: 0.7436 (tt) REVERT: C 188 ILE cc_start: 0.9280 (mt) cc_final: 0.9072 (mm) REVERT: C 404 MET cc_start: 0.8651 (ttt) cc_final: 0.8053 (tpp) REVERT: C 411 MET cc_start: 0.6339 (tpt) cc_final: 0.5819 (mmp) REVERT: C 414 TRP cc_start: 0.8853 (m100) cc_final: 0.8373 (m100) REVERT: E 77 MET cc_start: 0.8210 (tpp) cc_final: 0.7923 (tpp) REVERT: E 126 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7680 (pp20) REVERT: E 128 SER cc_start: 0.8503 (p) cc_final: 0.7540 (p) REVERT: E 170 MET cc_start: 0.8459 (mmm) cc_final: 0.8237 (mmm) REVERT: E 200 GLN cc_start: 0.8711 (mp10) cc_final: 0.8209 (mp10) REVERT: E 235 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7068 (tm-30) REVERT: E 310 TRP cc_start: 0.9275 (t-100) cc_final: 0.9021 (t-100) REVERT: E 324 GLU cc_start: 0.8359 (pp20) cc_final: 0.7918 (mm-30) REVERT: E 329 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8536 (mm-40) REVERT: E 465 PHE cc_start: 0.8343 (p90) cc_final: 0.7432 (p90) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2095 time to fit residues: 117.1862 Evaluate side-chains 300 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 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 177 GLN A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** 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** E 138 ASN ** E 208 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 = 0.3653 r_free = 0.3653 target = 0.113037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091189 restraints weight = 37340.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094103 restraints weight = 20572.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096070 restraints weight = 13652.498| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14163 Z= 0.246 Angle : 0.795 11.277 19179 Z= 0.406 Chirality : 0.050 0.367 2138 Planarity : 0.005 0.040 2386 Dihedral : 7.821 106.369 1981 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1662 helix: 1.63 (0.22), residues: 575 sheet: -0.56 (0.31), residues: 309 loop : -1.66 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 89 HIS 0.005 0.001 HIS C 201 PHE 0.032 0.002 PHE D 242 TYR 0.034 0.002 TYR A 301 ARG 0.007 0.001 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 1.83572 ( 15) hydrogen bonds : bond 0.04549 ( 653) hydrogen bonds : angle 4.78036 ( 1932) SS BOND : bond 0.00281 ( 10) SS BOND : angle 2.84950 ( 20) covalent geometry : bond 0.00558 (14148) covalent geometry : angle 0.78918 (19144) *********************** 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 362 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 LEU cc_start: 0.9352 (tp) cc_final: 0.9150 (tp) REVERT: D 141 ASP cc_start: 0.9129 (t0) cc_final: 0.8760 (t0) REVERT: D 404 MET cc_start: 0.8478 (tmm) cc_final: 0.8110 (tmm) REVERT: D 408 ILE cc_start: 0.9148 (tp) cc_final: 0.8845 (tp) REVERT: D 412 PHE cc_start: 0.8448 (m-80) cc_final: 0.8109 (m-10) REVERT: A 274 LEU cc_start: 0.9544 (mp) cc_final: 0.9136 (tt) REVERT: A 287 MET cc_start: 0.9356 (mmm) cc_final: 0.8780 (mmm) REVERT: B 97 ASP cc_start: 0.8317 (p0) cc_final: 0.7740 (p0) REVERT: B 103 GLU cc_start: 0.7912 (pp20) cc_final: 0.7505 (pp20) REVERT: B 110 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7358 (pt0) REVERT: B 163 MET cc_start: 0.8298 (mmp) cc_final: 0.7915 (mmp) REVERT: B 226 GLN cc_start: 0.8837 (tp40) cc_final: 0.8607 (tm-30) REVERT: B 239 TRP cc_start: 0.8372 (m-10) cc_final: 0.8096 (m-10) REVERT: B 242 PHE cc_start: 0.8195 (m-80) cc_final: 0.7836 (m-80) REVERT: B 279 TYR cc_start: 0.8058 (p90) cc_final: 0.7365 (p90) REVERT: C 17 LEU cc_start: 0.9302 (tp) cc_final: 0.8913 (tp) REVERT: C 18 MET cc_start: 0.8585 (pmm) cc_final: 0.8007 (pmm) REVERT: C 97 ASP cc_start: 0.7939 (p0) cc_final: 0.7238 (p0) REVERT: C 102 ASN cc_start: 0.8491 (p0) cc_final: 0.7820 (p0) REVERT: C 103 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 163 MET cc_start: 0.8491 (ptm) cc_final: 0.8246 (ptm) REVERT: C 192 GLU cc_start: 0.8403 (pm20) cc_final: 0.8187 (pm20) REVERT: C 404 MET cc_start: 0.8611 (ttt) cc_final: 0.8032 (tpp) REVERT: C 411 MET cc_start: 0.6354 (tpt) cc_final: 0.5877 (mmp) REVERT: C 414 TRP cc_start: 0.8981 (m100) cc_final: 0.8342 (m100) REVERT: E 77 MET cc_start: 0.8244 (tpp) cc_final: 0.7976 (tpp) REVERT: E 115 CYS cc_start: 0.8702 (t) cc_final: 0.8414 (t) REVERT: E 200 GLN cc_start: 0.8664 (mp10) cc_final: 0.8397 (mp-120) REVERT: E 208 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8592 (mm-40) REVERT: E 235 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 243 GLN cc_start: 0.7876 (pp30) cc_final: 0.7640 (pm20) REVERT: E 310 TRP cc_start: 0.9245 (t-100) cc_final: 0.8966 (t-100) REVERT: E 329 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8562 (mm-40) REVERT: E 465 PHE cc_start: 0.8361 (p90) cc_final: 0.7395 (p90) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2090 time to fit residues: 116.7324 Evaluate side-chains 306 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 119 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN A 61 ASN A 171 GLN ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** 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** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 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 = 0.3719 r_free = 0.3719 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.095744 restraints weight = 37232.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098805 restraints weight = 20424.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100886 restraints weight = 13442.208| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2868 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= 0.145 Angle : 0.764 13.384 19179 Z= 0.378 Chirality : 0.048 0.281 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.553 103.416 1981 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1662 helix: 1.69 (0.22), residues: 576 sheet: -0.45 (0.31), residues: 310 loop : -1.60 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.005 0.001 HIS C 201 PHE 0.030 0.002 PHE D 242 TYR 0.034 0.001 TYR A 301 ARG 0.007 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 5) link_NAG-ASN : angle 1.60179 ( 15) hydrogen bonds : bond 0.04095 ( 653) hydrogen bonds : angle 4.65230 ( 1932) SS BOND : bond 0.00346 ( 10) SS BOND : angle 2.50016 ( 20) covalent geometry : bond 0.00333 (14148) covalent geometry : angle 0.75885 (19144) ********************** 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 365 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9084 (t0) cc_final: 0.8671 (t0) REVERT: D 287 MET cc_start: 0.9158 (mmm) cc_final: 0.8825 (mmm) REVERT: D 404 MET cc_start: 0.8447 (tmm) cc_final: 0.8084 (tmm) REVERT: D 408 ILE cc_start: 0.9135 (tp) cc_final: 0.8840 (tp) REVERT: D 412 PHE cc_start: 0.8468 (m-80) cc_final: 0.8167 (m-10) REVERT: A 107 HIS cc_start: 0.8645 (p90) cc_final: 0.7904 (p90) REVERT: A 220 MET cc_start: 0.7395 (pmm) cc_final: 0.7150 (pmm) REVERT: A 246 MET cc_start: 0.9233 (ppp) cc_final: 0.8693 (ppp) REVERT: A 274 LEU cc_start: 0.9544 (mp) cc_final: 0.9140 (tt) REVERT: A 287 MET cc_start: 0.9372 (mmm) cc_final: 0.8704 (mmm) REVERT: B 57 ASP cc_start: 0.8282 (p0) cc_final: 0.8063 (p0) REVERT: B 97 ASP cc_start: 0.8225 (p0) cc_final: 0.7678 (p0) REVERT: B 163 MET cc_start: 0.8174 (mmp) cc_final: 0.7781 (mmp) REVERT: B 211 GLU cc_start: 0.7394 (mp0) cc_final: 0.7127 (mp0) REVERT: B 215 HIS cc_start: 0.7283 (m-70) cc_final: 0.6958 (m170) REVERT: B 226 GLN cc_start: 0.8770 (tp40) cc_final: 0.8382 (tp-100) REVERT: B 239 TRP cc_start: 0.8164 (m-10) cc_final: 0.7912 (m-10) REVERT: B 242 PHE cc_start: 0.8095 (m-80) cc_final: 0.7824 (m-80) REVERT: C 17 LEU cc_start: 0.9279 (tp) cc_final: 0.8917 (tp) REVERT: C 18 MET cc_start: 0.8564 (pmm) cc_final: 0.8075 (pmm) REVERT: C 97 ASP cc_start: 0.7724 (p0) cc_final: 0.7024 (p0) REVERT: C 102 ASN cc_start: 0.8483 (p0) cc_final: 0.7835 (p0) REVERT: C 103 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 163 MET cc_start: 0.8457 (ptm) cc_final: 0.8173 (ptm) REVERT: C 188 ILE cc_start: 0.9256 (mt) cc_final: 0.9036 (mm) REVERT: C 192 GLU cc_start: 0.8394 (pm20) cc_final: 0.7830 (tm-30) REVERT: C 404 MET cc_start: 0.8578 (ttt) cc_final: 0.8019 (tpp) REVERT: C 411 MET cc_start: 0.6298 (tpt) cc_final: 0.5815 (mmp) REVERT: C 414 TRP cc_start: 0.8896 (m100) cc_final: 0.8438 (m100) REVERT: E 77 MET cc_start: 0.8210 (tpp) cc_final: 0.7862 (tpp) REVERT: E 200 GLN cc_start: 0.8677 (mp10) cc_final: 0.8294 (mp-120) REVERT: E 235 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7148 (tm-30) REVERT: E 310 TRP cc_start: 0.9252 (t-100) cc_final: 0.8999 (t-100) REVERT: E 324 GLU cc_start: 0.8101 (pp20) cc_final: 0.7817 (mm-30) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2156 time to fit residues: 121.2007 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 : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.0050 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN 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** ** E 173 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 = 0.3757 r_free = 0.3757 target = 0.119814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098228 restraints weight = 37068.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101387 restraints weight = 20063.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103489 restraints weight = 13099.197| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14163 Z= 0.135 Angle : 0.753 11.969 19179 Z= 0.370 Chirality : 0.048 0.271 2138 Planarity : 0.004 0.043 2386 Dihedral : 7.278 101.196 1981 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1662 helix: 1.65 (0.22), residues: 573 sheet: -0.33 (0.32), residues: 299 loop : -1.59 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 170 HIS 0.005 0.001 HIS C 201 PHE 0.031 0.002 PHE D 242 TYR 0.032 0.001 TYR A 301 ARG 0.006 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 5) link_NAG-ASN : angle 1.55736 ( 15) hydrogen bonds : bond 0.03888 ( 653) hydrogen bonds : angle 4.54573 ( 1932) SS BOND : bond 0.00312 ( 10) SS BOND : angle 2.42691 ( 20) covalent geometry : bond 0.00307 (14148) covalent geometry : angle 0.74805 (19144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4672.40 seconds wall clock time: 81 minutes 43.90 seconds (4903.90 seconds total)