Starting phenix.real_space_refine on Mon Dec 30 23:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn4_27554/12_2024/8dn4_27554_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn4_27554/12_2024/8dn4_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_27554/12_2024/8dn4_27554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn4_27554/12_2024/8dn4_27554.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn4_27554/12_2024/8dn4_27554_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn4_27554/12_2024/8dn4_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-5532/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: 8.90, per 1000 atoms: 0.64 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 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: 1.58 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: 4.17 Time building geometry restraints manager: 3.95 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: 1.180 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.920 Find NCS groups from input model: 0.660 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- 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 14148 Z= 0.228 Angle : 0.723 7.597 19144 Z= 0.378 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 *********************** 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 : 1.699 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: 0.2368 time to fit residues: 152.5879 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 : 1.698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 14148 Z= 0.250 Angle : 0.697 10.386 19144 Z= 0.358 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 *********************** 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 : 1.600 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: 0.9296 (tp) cc_final: 0.8618 (tp) REVERT: D 18 MET cc_start: 0.9150 (pmm) cc_final: 0.8833 (pmm) REVERT: D 89 MET cc_start: 0.9436 (mmm) cc_final: 0.9114 (mpp) REVERT: D 404 MET cc_start: 0.8549 (tmm) cc_final: 0.8257 (tmm) REVERT: D 408 ILE cc_start: 0.9269 (tp) cc_final: 0.8954 (tp) REVERT: D 412 PHE cc_start: 0.8490 (m-80) cc_final: 0.8067 (m-10) REVERT: A 107 HIS cc_start: 0.8425 (p90) cc_final: 0.7954 (p90) REVERT: A 155 GLN cc_start: 0.8421 (mt0) cc_final: 0.7979 (mt0) REVERT: A 211 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 220 MET cc_start: 0.7611 (pmm) cc_final: 0.7390 (pmm) REVERT: A 274 LEU cc_start: 0.9512 (mp) cc_final: 0.9133 (tt) REVERT: A 287 MET cc_start: 0.9177 (mmm) cc_final: 0.8521 (mmm) REVERT: B 17 LEU cc_start: 0.9331 (tp) cc_final: 0.8825 (tp) REVERT: B 66 GLN cc_start: 0.9064 (mp-120) cc_final: 0.8843 (mp10) REVERT: B 103 GLU cc_start: 0.7850 (pp20) cc_final: 0.7529 (pp20) REVERT: B 173 GLN cc_start: 0.8983 (mp10) cc_final: 0.8578 (mp10) REVERT: B 210 ILE cc_start: 0.9436 (pt) cc_final: 0.9170 (pt) REVERT: B 211 GLU cc_start: 0.7516 (pm20) cc_final: 0.6621 (pm20) REVERT: B 235 VAL cc_start: 0.9565 (p) cc_final: 0.8775 (p) REVERT: B 239 TRP cc_start: 0.8283 (m-90) cc_final: 0.6964 (m-90) REVERT: C 17 LEU cc_start: 0.9285 (tp) cc_final: 0.9018 (tp) REVERT: C 18 MET cc_start: 0.8713 (pmm) cc_final: 0.8135 (pmm) REVERT: C 97 ASP cc_start: 0.7563 (p0) cc_final: 0.6917 (p0) REVERT: C 98 LEU cc_start: 0.9040 (tp) cc_final: 0.8837 (tp) REVERT: C 153 ILE cc_start: 0.8992 (pt) cc_final: 0.8670 (pt) REVERT: C 167 ILE cc_start: 0.7718 (tt) cc_final: 0.7304 (tt) REVERT: C 239 TRP cc_start: 0.7702 (m-10) cc_final: 0.7324 (m-10) REVERT: C 404 MET cc_start: 0.8694 (ttt) cc_final: 0.8313 (tpp) REVERT: C 411 MET cc_start: 0.6892 (tpt) cc_final: 0.6563 (mmp) REVERT: C 414 TRP cc_start: 0.8831 (m100) cc_final: 0.8571 (m100) REVERT: E 74 GLU cc_start: 0.8466 (mp0) cc_final: 0.8088 (mp0) REVERT: E 115 CYS cc_start: 0.8804 (t) cc_final: 0.8584 (t) REVERT: E 125 ASN cc_start: 0.8562 (m110) cc_final: 0.8230 (m110) REVERT: E 155 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9033 (pp) REVERT: E 170 MET cc_start: 0.8266 (mmm) cc_final: 0.7963 (mmm) REVERT: E 173 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7018 (mm110) REVERT: E 176 LYS cc_start: 0.9061 (ptmm) cc_final: 0.8463 (pttt) REVERT: E 314 CYS cc_start: 0.9286 (m) cc_final: 0.8996 (m) outliers start: 3 outliers final: 0 residues processed: 378 average time/residue: 0.2226 time to fit residues: 128.9477 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 : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 150 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14148 Z= 0.383 Angle : 0.749 11.373 19144 Z= 0.387 Chirality : 0.048 0.312 2138 Planarity : 0.005 0.055 2386 Dihedral : 8.482 110.751 1981 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.82 % Favored : 92.00 % Rotamer: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.90 % 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: -0.57 (0.21), residues: 1662 helix: 1.65 (0.22), residues: 574 sheet: -0.94 (0.30), residues: 312 loop : -1.75 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 310 HIS 0.006 0.002 HIS A 107 PHE 0.046 0.002 PHE B 242 TYR 0.019 0.002 TYR E 224 ARG 0.009 0.001 ARG C 29 *********************** 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 372 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9128 (t0) cc_final: 0.8761 (t0) REVERT: D 145 PHE cc_start: 0.9332 (t80) cc_final: 0.9079 (t80) REVERT: D 311 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.6468 (m-70) REVERT: D 404 MET cc_start: 0.8472 (tmm) cc_final: 0.8151 (tmm) REVERT: D 408 ILE cc_start: 0.9258 (tp) cc_final: 0.8973 (tp) REVERT: D 412 PHE cc_start: 0.8515 (m-80) cc_final: 0.8092 (m-10) REVERT: A 220 MET cc_start: 0.7682 (pmm) cc_final: 0.7359 (pmm) REVERT: A 246 MET cc_start: 0.9368 (ppp) cc_final: 0.9055 (ppp) REVERT: A 274 LEU cc_start: 0.9523 (mp) cc_final: 0.9149 (tt) REVERT: A 287 MET cc_start: 0.9184 (mmm) cc_final: 0.8514 (mmm) REVERT: B 17 LEU cc_start: 0.9352 (tp) cc_final: 0.8971 (tp) REVERT: B 66 GLN cc_start: 0.9095 (mp-120) cc_final: 0.8742 (mp10) REVERT: B 103 GLU cc_start: 0.8029 (pp20) cc_final: 0.7634 (pp20) REVERT: B 157 GLU cc_start: 0.8355 (pt0) cc_final: 0.7789 (pt0) REVERT: B 220 MET cc_start: 0.7804 (pmm) cc_final: 0.7430 (pmm) REVERT: B 242 PHE cc_start: 0.8072 (m-80) cc_final: 0.7811 (m-80) REVERT: B 263 MET cc_start: 0.9358 (tpt) cc_final: 0.9157 (tpt) REVERT: C 15 ASP cc_start: 0.8379 (t0) cc_final: 0.8098 (t0) REVERT: C 17 LEU cc_start: 0.9311 (tp) cc_final: 0.8897 (tp) REVERT: C 18 MET cc_start: 0.8672 (pmm) cc_final: 0.7996 (pmm) REVERT: C 97 ASP cc_start: 0.7841 (p0) cc_final: 0.7216 (p0) REVERT: C 167 ILE cc_start: 0.7969 (tt) cc_final: 0.7526 (tt) REVERT: C 238 SER cc_start: 0.8287 (p) cc_final: 0.8059 (p) REVERT: C 283 ILE cc_start: 0.8208 (tt) cc_final: 0.7333 (tp) REVERT: C 404 MET cc_start: 0.8660 (ttt) cc_final: 0.8094 (tpp) REVERT: C 411 MET cc_start: 0.6564 (tpt) cc_final: 0.6202 (mmp) REVERT: C 414 TRP cc_start: 0.8964 (m100) cc_final: 0.8711 (m100) REVERT: E 77 MET cc_start: 0.8299 (tpp) cc_final: 0.8031 (tpp) REVERT: E 115 CYS cc_start: 0.8799 (t) cc_final: 0.8545 (t) REVERT: E 173 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7402 (mm110) REVERT: E 200 GLN cc_start: 0.8631 (mp10) cc_final: 0.8297 (mp-120) REVERT: E 201 LEU cc_start: 0.7103 (tp) cc_final: 0.6845 (tp) REVERT: E 314 CYS cc_start: 0.9325 (m) cc_final: 0.9074 (m) REVERT: E 465 PHE cc_start: 0.8219 (p90) cc_final: 0.7964 (p90) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.2365 time to fit residues: 133.9321 Evaluate side-chains 293 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 0.4980 chunk 160 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** 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** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 138 ASN E 329 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14148 Z= 0.207 Angle : 0.688 10.045 19144 Z= 0.348 Chirality : 0.046 0.329 2138 Planarity : 0.004 0.047 2386 Dihedral : 7.977 108.099 1981 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % 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: -0.42 (0.21), residues: 1662 helix: 1.72 (0.22), residues: 574 sheet: -0.73 (0.30), residues: 309 loop : -1.67 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 239 HIS 0.007 0.001 HIS C 201 PHE 0.033 0.002 PHE E 282 TYR 0.015 0.001 TYR B 197 ARG 0.006 0.000 ARG C 29 *********************** 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 388 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9065 (t0) cc_final: 0.8837 (t0) REVERT: D 148 ASP cc_start: 0.8922 (t0) cc_final: 0.8287 (t0) REVERT: D 196 ARG cc_start: 0.8321 (ptt180) cc_final: 0.8055 (ptt90) REVERT: D 226 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 404 MET cc_start: 0.8447 (tmm) cc_final: 0.8115 (tmm) REVERT: D 408 ILE cc_start: 0.9196 (tp) cc_final: 0.8858 (tp) REVERT: D 412 PHE cc_start: 0.8484 (m-80) cc_final: 0.8228 (m-80) REVERT: A 220 MET cc_start: 0.7509 (pmm) cc_final: 0.7098 (pmm) REVERT: A 274 LEU cc_start: 0.9474 (mp) cc_final: 0.9127 (tt) REVERT: A 287 MET cc_start: 0.9191 (mmm) cc_final: 0.8492 (mmm) REVERT: A 306 PHE cc_start: 0.8646 (t80) cc_final: 0.8244 (t80) REVERT: B 97 ASP cc_start: 0.8128 (p0) cc_final: 0.7619 (p0) REVERT: B 220 MET cc_start: 0.7588 (pmm) cc_final: 0.7218 (pmm) REVERT: B 239 TRP cc_start: 0.8238 (m-90) cc_final: 0.6874 (m-90) REVERT: B 242 PHE cc_start: 0.8025 (m-80) cc_final: 0.7778 (m-80) REVERT: C 17 LEU cc_start: 0.9277 (tp) cc_final: 0.8888 (tp) REVERT: C 18 MET cc_start: 0.8727 (pmm) cc_final: 0.8047 (pmm) REVERT: C 97 ASP cc_start: 0.7736 (p0) cc_final: 0.7047 (p0) REVERT: C 102 ASN cc_start: 0.8256 (p0) cc_final: 0.7685 (p0) REVERT: C 103 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 404 MET cc_start: 0.8668 (ttt) cc_final: 0.8072 (tpp) REVERT: C 411 MET cc_start: 0.6435 (tpt) cc_final: 0.6058 (mmp) REVERT: C 414 TRP cc_start: 0.8852 (m100) cc_final: 0.8628 (m100) REVERT: E 77 MET cc_start: 0.8217 (tpp) cc_final: 0.7947 (tpp) REVERT: E 115 CYS cc_start: 0.8681 (t) cc_final: 0.8435 (t) REVERT: E 170 MET cc_start: 0.8315 (mmm) cc_final: 0.7947 (mmm) REVERT: E 173 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7395 (mm110) REVERT: E 200 GLN cc_start: 0.8618 (mp10) cc_final: 0.8055 (mp10) REVERT: E 234 VAL cc_start: 0.8657 (m) cc_final: 0.8353 (m) REVERT: E 235 GLU cc_start: 0.7745 (tm-30) cc_final: 0.6946 (tm-30) REVERT: E 310 TRP cc_start: 0.9262 (t-100) cc_final: 0.8974 (t-100) REVERT: E 314 CYS cc_start: 0.9218 (m) cc_final: 0.8753 (m) REVERT: E 465 PHE cc_start: 0.8233 (p90) cc_final: 0.7048 (p90) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.2661 time to fit residues: 156.5358 Evaluate side-chains 312 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.0770 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 0.0270 chunk 66 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- 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 150 GLN D 155 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 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14148 Z= 0.219 Angle : 0.679 10.362 19144 Z= 0.344 Chirality : 0.046 0.314 2138 Planarity : 0.004 0.043 2386 Dihedral : 7.868 107.050 1981 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.38 % Favored : 93.44 % Rotamer: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % 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: -0.42 (0.21), residues: 1662 helix: 1.62 (0.22), residues: 574 sheet: -0.63 (0.30), residues: 309 loop : -1.64 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 239 HIS 0.006 0.001 HIS C 201 PHE 0.034 0.002 PHE E 282 TYR 0.013 0.001 TYR C 413 ARG 0.008 0.000 ARG A 29 *********************** 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 373 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8997 (t0) cc_final: 0.8771 (t0) REVERT: D 287 MET cc_start: 0.9120 (mmm) cc_final: 0.8680 (mmm) REVERT: D 404 MET cc_start: 0.8470 (tmm) cc_final: 0.8150 (tmm) REVERT: D 408 ILE cc_start: 0.9199 (tp) cc_final: 0.8847 (tp) REVERT: D 412 PHE cc_start: 0.8467 (m-80) cc_final: 0.8226 (m-80) REVERT: A 220 MET cc_start: 0.7526 (pmm) cc_final: 0.7113 (pmm) REVERT: A 262 THR cc_start: 0.9534 (p) cc_final: 0.8790 (p) REVERT: A 263 MET cc_start: 0.8694 (mmm) cc_final: 0.8335 (mmp) REVERT: A 274 LEU cc_start: 0.9479 (mp) cc_final: 0.9123 (tt) REVERT: A 287 MET cc_start: 0.9323 (mmm) cc_final: 0.8520 (mmm) REVERT: A 306 PHE cc_start: 0.8659 (t80) cc_final: 0.8247 (t80) REVERT: B 66 GLN cc_start: 0.8890 (mp-120) cc_final: 0.8629 (mp10) REVERT: B 97 ASP cc_start: 0.8128 (p0) cc_final: 0.7558 (p0) REVERT: B 220 MET cc_start: 0.7591 (pmm) cc_final: 0.7225 (pmm) REVERT: B 235 VAL cc_start: 0.9527 (p) cc_final: 0.8671 (p) REVERT: B 239 TRP cc_start: 0.8230 (m-90) cc_final: 0.6792 (m-90) REVERT: B 242 PHE cc_start: 0.8089 (m-80) cc_final: 0.7845 (m-80) REVERT: C 17 LEU cc_start: 0.9299 (tp) cc_final: 0.8909 (tp) REVERT: C 18 MET cc_start: 0.8677 (pmm) cc_final: 0.8013 (pmm) REVERT: C 97 ASP cc_start: 0.7779 (p0) cc_final: 0.7100 (p0) REVERT: C 102 ASN cc_start: 0.8327 (p0) cc_final: 0.7690 (p0) REVERT: C 167 ILE cc_start: 0.7737 (tt) cc_final: 0.7382 (tt) REVERT: C 404 MET cc_start: 0.8653 (ttt) cc_final: 0.8055 (tpp) REVERT: C 411 MET cc_start: 0.6506 (tpt) cc_final: 0.6013 (mmp) REVERT: E 115 CYS cc_start: 0.8684 (t) cc_final: 0.8449 (t) REVERT: E 170 MET cc_start: 0.8324 (mmm) cc_final: 0.7957 (mmm) REVERT: E 173 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7304 (mm110) REVERT: E 200 GLN cc_start: 0.8663 (mp10) cc_final: 0.8041 (mp10) REVERT: E 234 VAL cc_start: 0.8561 (m) cc_final: 0.8353 (m) REVERT: E 235 GLU cc_start: 0.7818 (tm-30) cc_final: 0.6935 (tm-30) REVERT: E 310 TRP cc_start: 0.9215 (t-100) cc_final: 0.8987 (t-100) REVERT: E 324 GLU cc_start: 0.8170 (pp20) cc_final: 0.7848 (mm-30) REVERT: E 329 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8533 (mm-40) REVERT: E 465 PHE cc_start: 0.8306 (p90) cc_final: 0.7232 (p90) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.2318 time to fit residues: 130.4711 Evaluate side-chains 303 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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** A 61 ASN A 171 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14148 Z= 0.277 Angle : 0.706 9.657 19144 Z= 0.360 Chirality : 0.047 0.343 2138 Planarity : 0.004 0.042 2386 Dihedral : 7.717 107.137 1981 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.62 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 1.59 (0.22), residues: 574 sheet: -0.71 (0.30), residues: 309 loop : -1.65 (0.22), residues: 779 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 0.037 0.002 PHE E 282 TYR 0.023 0.001 TYR A 301 ARG 0.006 0.001 ARG C 29 *********************** 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 375 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.609 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 140 MET cc_start: 0.7838 (mmm) cc_final: 0.7134 (mmp) REVERT: D 141 ASP cc_start: 0.9121 (t0) cc_final: 0.8744 (t0) REVERT: D 404 MET cc_start: 0.8494 (tmm) cc_final: 0.8158 (tmm) REVERT: D 408 ILE cc_start: 0.9170 (tp) cc_final: 0.8879 (tp) REVERT: D 412 PHE cc_start: 0.8479 (m-80) cc_final: 0.8112 (m-10) REVERT: A 220 MET cc_start: 0.7562 (pmm) cc_final: 0.7156 (pmm) REVERT: A 263 MET cc_start: 0.8560 (mmm) cc_final: 0.8083 (mmp) REVERT: A 274 LEU cc_start: 0.9506 (mp) cc_final: 0.9158 (tt) REVERT: A 287 MET cc_start: 0.9271 (mmm) cc_final: 0.8630 (mmm) REVERT: B 66 GLN cc_start: 0.8943 (mp-120) cc_final: 0.8671 (mp10) REVERT: B 97 ASP cc_start: 0.8237 (p0) cc_final: 0.7656 (p0) REVERT: B 103 GLU cc_start: 0.7916 (pp20) cc_final: 0.7515 (pp20) REVERT: B 110 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7456 (pt0) REVERT: B 142 LEU cc_start: 0.9382 (mp) cc_final: 0.9071 (mp) REVERT: B 220 MET cc_start: 0.7716 (pmm) cc_final: 0.7369 (pmm) REVERT: B 235 VAL cc_start: 0.9556 (p) cc_final: 0.8550 (p) REVERT: B 239 TRP cc_start: 0.8302 (m-90) cc_final: 0.6871 (m-90) REVERT: B 279 TYR cc_start: 0.8126 (p90) cc_final: 0.7418 (p90) REVERT: C 17 LEU cc_start: 0.9287 (tp) cc_final: 0.8921 (tp) REVERT: C 18 MET cc_start: 0.8578 (pmm) cc_final: 0.8004 (pmm) REVERT: C 97 ASP cc_start: 0.7861 (p0) cc_final: 0.7173 (p0) REVERT: C 102 ASN cc_start: 0.8335 (p0) cc_final: 0.7729 (p0) REVERT: C 103 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 167 ILE cc_start: 0.7885 (tt) cc_final: 0.7497 (tt) REVERT: C 283 ILE cc_start: 0.8320 (tt) cc_final: 0.7281 (tp) REVERT: C 300 GLU cc_start: 0.8968 (pp20) cc_final: 0.8624 (pp20) REVERT: C 404 MET cc_start: 0.8644 (ttt) cc_final: 0.8011 (tpp) REVERT: C 411 MET cc_start: 0.6510 (tpt) cc_final: 0.5981 (mmp) REVERT: E 115 CYS cc_start: 0.8679 (t) cc_final: 0.8427 (t) REVERT: E 170 MET cc_start: 0.8352 (mmm) cc_final: 0.8029 (mmm) REVERT: E 173 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7524 (mm110) REVERT: E 200 GLN cc_start: 0.8663 (mp10) cc_final: 0.8130 (mp10) REVERT: E 234 VAL cc_start: 0.8547 (m) cc_final: 0.8223 (m) REVERT: E 235 GLU cc_start: 0.7825 (tm-30) cc_final: 0.6969 (tm-30) REVERT: E 310 TRP cc_start: 0.9216 (t-100) cc_final: 0.8985 (t-100) REVERT: E 329 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8526 (mm-40) REVERT: E 465 PHE cc_start: 0.8312 (p90) cc_final: 0.7258 (p90) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2387 time to fit residues: 134.1704 Evaluate side-chains 299 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 98 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14148 Z= 0.356 Angle : 0.761 11.648 19144 Z= 0.391 Chirality : 0.048 0.290 2138 Planarity : 0.005 0.041 2386 Dihedral : 7.917 108.373 1981 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % 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 : 0.13 % 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: -0.58 (0.21), residues: 1662 helix: 1.54 (0.22), residues: 573 sheet: -0.86 (0.30), residues: 310 loop : -1.70 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 414 HIS 0.006 0.001 HIS C 201 PHE 0.039 0.002 PHE D 293 TYR 0.021 0.002 TYR B 301 ARG 0.007 0.001 ARG B 27 *********************** 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 365 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9123 (t0) cc_final: 0.8719 (t0) REVERT: D 287 MET cc_start: 0.9153 (mmm) cc_final: 0.8772 (mmm) REVERT: D 404 MET cc_start: 0.8495 (tmm) cc_final: 0.8125 (tmm) REVERT: D 408 ILE cc_start: 0.9152 (tp) cc_final: 0.8850 (tp) REVERT: D 412 PHE cc_start: 0.8496 (m-80) cc_final: 0.8101 (m-10) REVERT: A 89 MET cc_start: 0.9125 (mmm) cc_final: 0.8921 (mmm) REVERT: A 246 MET cc_start: 0.9220 (ppp) cc_final: 0.8951 (ppp) REVERT: A 287 MET cc_start: 0.9318 (mmm) cc_final: 0.8755 (mmm) REVERT: B 66 GLN cc_start: 0.8950 (mp-120) cc_final: 0.8683 (mp10) REVERT: B 97 ASP cc_start: 0.8306 (p0) cc_final: 0.7718 (p0) REVERT: B 103 GLU cc_start: 0.7951 (pp20) cc_final: 0.7588 (pp20) REVERT: B 110 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7486 (pt0) REVERT: B 142 LEU cc_start: 0.9428 (mp) cc_final: 0.9119 (mp) REVERT: B 163 MET cc_start: 0.8319 (mmp) cc_final: 0.7930 (mmp) REVERT: B 220 MET cc_start: 0.7858 (pmm) cc_final: 0.7584 (pmm) REVERT: B 242 PHE cc_start: 0.8128 (m-80) cc_final: 0.7778 (m-80) REVERT: B 279 TYR cc_start: 0.8122 (p90) cc_final: 0.7388 (p90) REVERT: B 415 ILE cc_start: 0.8903 (tp) cc_final: 0.8683 (tp) REVERT: C 17 LEU cc_start: 0.9294 (tp) cc_final: 0.8909 (tp) REVERT: C 18 MET cc_start: 0.8615 (pmm) cc_final: 0.8043 (pmm) REVERT: C 97 ASP cc_start: 0.7936 (p0) cc_final: 0.7250 (p0) REVERT: C 102 ASN cc_start: 0.8441 (p0) cc_final: 0.7790 (p0) REVERT: C 103 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 167 ILE cc_start: 0.7965 (tt) cc_final: 0.7523 (tt) REVERT: C 169 GLU cc_start: 0.7038 (mp0) cc_final: 0.6643 (mp0) REVERT: C 242 PHE cc_start: 0.7579 (m-80) cc_final: 0.6993 (m-80) REVERT: C 404 MET cc_start: 0.8625 (ttt) cc_final: 0.8033 (tpp) REVERT: C 411 MET cc_start: 0.6385 (tpt) cc_final: 0.5904 (mmp) REVERT: E 74 GLU cc_start: 0.8246 (mp0) cc_final: 0.7937 (mp0) REVERT: E 77 MET cc_start: 0.8017 (tpp) cc_final: 0.7763 (tpp) REVERT: E 115 CYS cc_start: 0.8699 (t) cc_final: 0.8393 (t) REVERT: E 170 MET cc_start: 0.8350 (mmm) cc_final: 0.8083 (mmm) REVERT: E 200 GLN cc_start: 0.8660 (mp10) cc_final: 0.8247 (mp10) REVERT: E 234 VAL cc_start: 0.8570 (m) cc_final: 0.8226 (m) REVERT: E 235 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7144 (tm-30) REVERT: E 310 TRP cc_start: 0.9262 (t-100) cc_final: 0.8951 (t-100) REVERT: E 465 PHE cc_start: 0.8308 (p90) cc_final: 0.7170 (p90) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2205 time to fit residues: 123.4623 Evaluate side-chains 296 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14148 Z= 0.204 Angle : 0.734 13.356 19144 Z= 0.368 Chirality : 0.048 0.274 2138 Planarity : 0.004 0.041 2386 Dihedral : 7.560 104.916 1981 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.44 (0.21), residues: 1662 helix: 1.63 (0.22), residues: 574 sheet: -0.66 (0.30), residues: 309 loop : -1.66 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 286 HIS 0.006 0.001 HIS C 201 PHE 0.035 0.002 PHE E 282 TYR 0.018 0.001 TYR B 301 ARG 0.007 0.000 ARG B 29 *********************** 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 375 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.647 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: D 103 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 141 ASP cc_start: 0.9026 (t0) cc_final: 0.8732 (t0) REVERT: D 154 MET cc_start: 0.8784 (mtm) cc_final: 0.8332 (mtm) REVERT: D 287 MET cc_start: 0.9182 (mmm) cc_final: 0.8780 (mmm) REVERT: D 404 MET cc_start: 0.8460 (tmm) cc_final: 0.8093 (tmm) REVERT: D 408 ILE cc_start: 0.9133 (tp) cc_final: 0.8831 (tp) REVERT: D 412 PHE cc_start: 0.8485 (m-80) cc_final: 0.8128 (m-10) REVERT: A 220 MET cc_start: 0.7594 (pmm) cc_final: 0.7258 (pmm) REVERT: A 274 LEU cc_start: 0.9459 (mp) cc_final: 0.9115 (tt) REVERT: A 287 MET cc_start: 0.9300 (mmm) cc_final: 0.8591 (mmm) REVERT: A 404 MET cc_start: 0.8019 (tmm) cc_final: 0.7792 (tmm) REVERT: B 66 GLN cc_start: 0.8844 (mp-120) cc_final: 0.8556 (mp10) REVERT: B 97 ASP cc_start: 0.8134 (p0) cc_final: 0.7601 (p0) REVERT: B 211 GLU cc_start: 0.7383 (mp0) cc_final: 0.7081 (mp0) REVERT: B 220 MET cc_start: 0.7597 (pmm) cc_final: 0.7242 (pmm) REVERT: B 239 TRP cc_start: 0.8203 (m-10) cc_final: 0.6672 (m-90) REVERT: B 242 PHE cc_start: 0.8058 (m-80) cc_final: 0.7819 (m-80) REVERT: C 97 ASP cc_start: 0.7748 (p0) cc_final: 0.7044 (p0) REVERT: C 102 ASN cc_start: 0.8421 (p0) cc_final: 0.7779 (p0) REVERT: C 103 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 167 ILE cc_start: 0.7724 (tt) cc_final: 0.7356 (tt) REVERT: C 242 PHE cc_start: 0.7398 (m-80) cc_final: 0.7062 (m-80) REVERT: C 404 MET cc_start: 0.8606 (ttt) cc_final: 0.8003 (tpp) REVERT: C 411 MET cc_start: 0.6386 (tpt) cc_final: 0.5879 (mmp) REVERT: E 77 MET cc_start: 0.7970 (tpp) cc_final: 0.7727 (tpp) REVERT: E 170 MET cc_start: 0.8418 (mmm) cc_final: 0.8001 (mmm) REVERT: E 173 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7118 (mm110) REVERT: E 200 GLN cc_start: 0.8648 (mp10) cc_final: 0.8282 (mp-120) REVERT: E 234 VAL cc_start: 0.8510 (m) cc_final: 0.8291 (m) REVERT: E 235 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7170 (tm-30) REVERT: E 310 TRP cc_start: 0.9284 (t-100) cc_final: 0.9015 (t-100) REVERT: E 324 GLU cc_start: 0.8157 (pp20) cc_final: 0.7844 (mm-30) REVERT: E 329 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8549 (mm-40) REVERT: E 465 PHE cc_start: 0.8287 (p90) cc_final: 0.7324 (p90) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2302 time to fit residues: 131.3193 Evaluate side-chains 311 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN A 186 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14148 Z= 0.215 Angle : 0.729 11.243 19144 Z= 0.366 Chirality : 0.047 0.369 2138 Planarity : 0.004 0.054 2386 Dihedral : 7.397 103.763 1981 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.08 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.42 (0.21), residues: 1662 helix: 1.58 (0.22), residues: 574 sheet: -0.57 (0.30), residues: 308 loop : -1.62 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 89 HIS 0.005 0.001 HIS C 201 PHE 0.032 0.002 PHE E 282 TYR 0.022 0.001 TYR B 301 ARG 0.010 0.000 ARG D 27 *********************** 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 377 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.668 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 103 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8373 (tm-30) REVERT: D 141 ASP cc_start: 0.9039 (t0) cc_final: 0.8687 (t0) REVERT: D 192 GLU cc_start: 0.7654 (pm20) cc_final: 0.7344 (pm20) REVERT: D 263 MET cc_start: 0.8328 (mmp) cc_final: 0.8039 (mmp) REVERT: D 287 MET cc_start: 0.9198 (mmm) cc_final: 0.8771 (mmm) REVERT: D 404 MET cc_start: 0.8455 (tmm) cc_final: 0.8099 (tmm) REVERT: D 408 ILE cc_start: 0.9144 (tp) cc_final: 0.8848 (tp) REVERT: D 412 PHE cc_start: 0.8477 (m-80) cc_final: 0.8168 (m-10) REVERT: A 220 MET cc_start: 0.7543 (pmm) cc_final: 0.7252 (pmm) REVERT: A 274 LEU cc_start: 0.9459 (mp) cc_final: 0.9103 (tt) REVERT: A 287 MET cc_start: 0.9354 (mmm) cc_final: 0.8686 (mmm) REVERT: A 404 MET cc_start: 0.8108 (tmm) cc_final: 0.7892 (tmm) REVERT: B 56 MET cc_start: 0.8426 (mmp) cc_final: 0.8186 (mmp) REVERT: B 57 ASP cc_start: 0.8183 (p0) cc_final: 0.7879 (p0) REVERT: B 66 GLN cc_start: 0.8848 (mp-120) cc_final: 0.8535 (mp10) REVERT: B 97 ASP cc_start: 0.8059 (p0) cc_final: 0.7512 (p0) REVERT: B 110 GLU cc_start: 0.8122 (pt0) cc_final: 0.7790 (pt0) REVERT: B 142 LEU cc_start: 0.9273 (mp) cc_final: 0.9058 (mp) REVERT: B 163 MET cc_start: 0.8198 (mmp) cc_final: 0.7856 (mmp) REVERT: B 211 GLU cc_start: 0.7395 (mp0) cc_final: 0.7135 (mp0) REVERT: B 226 GLN cc_start: 0.7283 (tt0) cc_final: 0.7014 (tt0) REVERT: B 239 TRP cc_start: 0.8176 (m-10) cc_final: 0.6655 (m-90) REVERT: C 97 ASP cc_start: 0.7682 (p0) cc_final: 0.6987 (p0) REVERT: C 102 ASN cc_start: 0.8427 (p0) cc_final: 0.7783 (p0) REVERT: C 103 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 188 ILE cc_start: 0.9289 (mt) cc_final: 0.9069 (mm) REVERT: C 242 PHE cc_start: 0.7405 (m-80) cc_final: 0.6976 (m-80) REVERT: C 404 MET cc_start: 0.8610 (ttt) cc_final: 0.7993 (tpp) REVERT: C 411 MET cc_start: 0.6366 (tpt) cc_final: 0.5803 (mmp) REVERT: E 74 GLU cc_start: 0.8275 (mp0) cc_final: 0.7971 (mp0) REVERT: E 77 MET cc_start: 0.7958 (tpp) cc_final: 0.7658 (tpp) REVERT: E 170 MET cc_start: 0.8401 (mmm) cc_final: 0.8031 (mmm) REVERT: E 173 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7065 (mm110) REVERT: E 200 GLN cc_start: 0.8641 (mp10) cc_final: 0.8269 (mp-120) REVERT: E 234 VAL cc_start: 0.8533 (m) cc_final: 0.8307 (m) REVERT: E 235 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7156 (tm-30) REVERT: E 310 TRP cc_start: 0.9271 (t-100) cc_final: 0.9061 (t-100) REVERT: E 324 GLU cc_start: 0.8296 (pp20) cc_final: 0.7920 (mm-30) REVERT: E 329 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8551 (mm-40) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2264 time to fit residues: 129.8799 Evaluate side-chains 312 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.0020 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN ** A 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14148 Z= 0.215 Angle : 0.746 12.931 19144 Z= 0.372 Chirality : 0.047 0.274 2138 Planarity : 0.004 0.045 2386 Dihedral : 7.466 102.942 1981 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.03 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: -0.42 (0.21), residues: 1662 helix: 1.55 (0.22), residues: 574 sheet: -0.54 (0.30), residues: 307 loop : -1.60 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 170 HIS 0.005 0.001 HIS B 215 PHE 0.031 0.002 PHE D 242 TYR 0.024 0.001 TYR B 301 ARG 0.009 0.000 ARG B 309 ********************** 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 381 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.9019 (t0) cc_final: 0.8692 (t0) REVERT: D 257 ILE cc_start: 0.8534 (mm) cc_final: 0.8293 (mm) REVERT: D 263 MET cc_start: 0.8303 (mmp) cc_final: 0.8079 (mmp) REVERT: D 287 MET cc_start: 0.9195 (mmm) cc_final: 0.8738 (mmm) REVERT: D 404 MET cc_start: 0.8461 (tmm) cc_final: 0.8103 (tmm) REVERT: D 408 ILE cc_start: 0.9150 (tp) cc_final: 0.8854 (tp) REVERT: D 412 PHE cc_start: 0.8473 (m-80) cc_final: 0.8166 (m-10) REVERT: A 220 MET cc_start: 0.7557 (pmm) cc_final: 0.7239 (pmm) REVERT: A 274 LEU cc_start: 0.9443 (mp) cc_final: 0.9099 (tt) REVERT: A 287 MET cc_start: 0.9307 (mmm) cc_final: 0.8625 (mmm) REVERT: A 404 MET cc_start: 0.8112 (tmm) cc_final: 0.7890 (tmm) REVERT: B 56 MET cc_start: 0.8395 (mmp) cc_final: 0.8143 (mmp) REVERT: B 57 ASP cc_start: 0.8036 (p0) cc_final: 0.7772 (p0) REVERT: B 97 ASP cc_start: 0.8020 (p0) cc_final: 0.7446 (p0) REVERT: B 110 GLU cc_start: 0.8173 (pt0) cc_final: 0.7824 (pt0) REVERT: B 163 MET cc_start: 0.8230 (mmp) cc_final: 0.7867 (mmp) REVERT: B 211 GLU cc_start: 0.7435 (mp0) cc_final: 0.7136 (mp0) REVERT: B 239 TRP cc_start: 0.8181 (m-10) cc_final: 0.6668 (m-90) REVERT: B 242 PHE cc_start: 0.7942 (m-80) cc_final: 0.7739 (m-80) REVERT: C 17 LEU cc_start: 0.9246 (tp) cc_final: 0.8654 (tp) REVERT: C 18 MET cc_start: 0.8551 (pmm) cc_final: 0.7788 (pmm) REVERT: C 97 ASP cc_start: 0.7679 (p0) cc_final: 0.7028 (p0) REVERT: C 102 ASN cc_start: 0.8424 (p0) cc_final: 0.7784 (p0) REVERT: C 103 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 163 MET cc_start: 0.8411 (ptm) cc_final: 0.8188 (ptm) REVERT: C 192 GLU cc_start: 0.8129 (pm20) cc_final: 0.7661 (tm-30) REVERT: C 404 MET cc_start: 0.8595 (ttt) cc_final: 0.7997 (tpp) REVERT: C 411 MET cc_start: 0.6254 (tpt) cc_final: 0.5762 (mmp) REVERT: E 74 GLU cc_start: 0.8224 (mp0) cc_final: 0.7961 (mp0) REVERT: E 115 CYS cc_start: 0.8804 (t) cc_final: 0.8603 (t) REVERT: E 170 MET cc_start: 0.8446 (mmm) cc_final: 0.8081 (mmm) REVERT: E 173 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7020 (mm110) REVERT: E 200 GLN cc_start: 0.8641 (mp10) cc_final: 0.8225 (mp-120) REVERT: E 234 VAL cc_start: 0.8522 (m) cc_final: 0.8305 (m) REVERT: E 235 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7158 (tm-30) REVERT: E 324 GLU cc_start: 0.8288 (pp20) cc_final: 0.7859 (mm-30) REVERT: E 329 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8562 (mm-40) REVERT: E 465 PHE cc_start: 0.8413 (p90) cc_final: 0.7444 (p90) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.2358 time to fit residues: 136.3418 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 : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 8.9990 chunk 40 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 171 GLN A 186 GLN ** 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 = 0.3757 r_free = 0.3757 target = 0.119692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098085 restraints weight = 36802.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101209 restraints weight = 20024.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103258 restraints weight = 13120.780| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14148 Z= 0.197 Angle : 0.739 10.402 19144 Z= 0.368 Chirality : 0.047 0.263 2138 Planarity : 0.004 0.043 2386 Dihedral : 7.255 101.114 1981 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.39 (0.21), residues: 1662 helix: 1.55 (0.22), residues: 573 sheet: -0.46 (0.30), residues: 307 loop : -1.59 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.005 0.001 HIS C 201 PHE 0.030 0.002 PHE D 242 TYR 0.020 0.001 TYR A 301 ARG 0.009 0.000 ARG C 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3317.63 seconds wall clock time: 61 minutes 52.88 seconds (3712.88 seconds total)