Starting phenix.real_space_refine on Thu Sep 26 19:27:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jaf_6346/09_2024/3jaf_6346.cif" } resolution = 3.8 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= -0.000 sd= 1.000 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 90 5.16 5 C 9115 2.51 5 N 2210 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13865 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.50, per 1000 atoms: 0.61 Number of scatterers: 13865 At special positions: 0 Unit cell: (95.68, 97.76, 127.92, 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 90 16.00 O 2450 8.00 N 2210 7.00 C 9115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.6% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.745A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 Processing helix chain 'B' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.745A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.535A pdb=" N TYR C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 Processing helix chain 'C' and resid 328 through 363 removed outlier: 3.600A pdb=" N THR C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.746A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 361 " --> pdb=" O TYR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.745A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 361 " --> pdb=" O TYR D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 254 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 290 " --> pdb=" O SER E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 Processing helix chain 'E' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.745A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=D, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=E, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.842A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=H, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=I, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=L, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=M, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=P, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=Q, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=T, first strand: chain 'E' and resid 115 through 116 836 hydrogen bonds defined for protein. 2418 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: 4.66 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4069 1.34 - 1.46: 2905 1.46 - 1.58: 7121 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14245 Sorted by residual: bond pdb=" C46 IVM E 401 " pdb=" O12 IVM E 401 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C46 IVM A 503 " pdb=" O12 IVM A 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C46 IVM B 503 " pdb=" O12 IVM B 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C46 IVM D 503 " pdb=" O12 IVM D 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C46 IVM C 503 " pdb=" O12 IVM C 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17654 2.12 - 4.24: 1504 4.24 - 6.36: 228 6.36 - 8.48: 54 8.48 - 10.60: 5 Bond angle restraints: 19445 Sorted by residual: angle pdb=" N GLY B 327 " pdb=" CA GLY B 327 " pdb=" C GLY B 327 " ideal model delta sigma weight residual 111.42 122.02 -10.60 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY C 327 " pdb=" CA GLY C 327 " pdb=" C GLY C 327 " ideal model delta sigma weight residual 111.42 122.01 -10.59 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY D 327 " pdb=" CA GLY D 327 " pdb=" C GLY D 327 " ideal model delta sigma weight residual 111.42 122.00 -10.58 1.51e+00 4.39e-01 4.91e+01 angle pdb=" N GLY E 327 " pdb=" CA GLY E 327 " pdb=" C GLY E 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 ... (remaining 19440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 8605 24.30 - 48.59: 220 48.59 - 72.89: 75 72.89 - 97.19: 40 97.19 - 121.48: 85 Dihedral angle restraints: 9025 sinusoidal: 3975 harmonic: 5050 Sorted by residual: dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.47 78.47 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 9022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2029 0.080 - 0.159: 250 0.159 - 0.239: 11 0.239 - 0.319: 5 0.319 - 0.399: 5 Chirality restraints: 2300 Sorted by residual: chirality pdb=" C47 IVM D 503 " pdb=" C39 IVM D 503 " pdb=" C41 IVM D 503 " pdb=" C45 IVM D 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C47 IVM C 503 " pdb=" C39 IVM C 503 " pdb=" C41 IVM C 503 " pdb=" C45 IVM C 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C47 IVM B 503 " pdb=" C39 IVM B 503 " pdb=" C41 IVM B 503 " pdb=" C45 IVM B 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 2297 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 265 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 265 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO B 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 265 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 266 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 266 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 266 " -0.029 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 322 2.69 - 3.24: 14524 3.24 - 3.79: 20992 3.79 - 4.35: 28592 4.35 - 4.90: 45301 Nonbonded interactions: 109731 Sorted by model distance: nonbonded pdb=" O SER E 254 " pdb=" OG SER E 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER D 254 " pdb=" OG SER D 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER B 254 " pdb=" OG SER B 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER C 254 " pdb=" OG SER C 257 " model vdw 2.135 3.040 ... (remaining 109726 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.080 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: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.290 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.006 0.127 14245 Z= 0.423 Angle : 1.345 10.595 19445 Z= 0.855 Chirality : 0.056 0.399 2300 Planarity : 0.005 0.054 2360 Dihedral : 18.829 121.482 5740 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.70 % Allowed : 1.06 % Favored : 98.24 % 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: -0.82 (0.18), residues: 1700 helix: -0.70 (0.20), residues: 540 sheet: 0.76 (0.25), residues: 340 loop : -0.92 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 259 HIS 0.003 0.001 HIS B 125 PHE 0.029 0.004 PHE E 29 TYR 0.026 0.003 TYR E 94 ARG 0.021 0.003 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 307 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6955 (m-30) cc_final: 0.6657 (m-30) REVERT: D 100 ASP cc_start: 0.6599 (m-30) cc_final: 0.6179 (m-30) REVERT: D 130 ASP cc_start: 0.6910 (t0) cc_final: 0.6700 (t0) REVERT: E 89 LEU cc_start: 0.8164 (mt) cc_final: 0.7917 (mt) REVERT: E 100 ASP cc_start: 0.7263 (m-30) cc_final: 0.6800 (m-30) REVERT: E 271 LEU cc_start: 0.8884 (mt) cc_final: 0.8672 (mt) outliers start: 10 outliers final: 0 residues processed: 317 average time/residue: 0.2279 time to fit residues: 109.3759 Evaluate side-chains 176 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0170 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 133 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 131 ASN A 354 ASN B 54 ASN B 131 ASN B 354 ASN C 54 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 354 ASN D 54 ASN D 131 ASN D 354 ASN E 54 ASN E 131 ASN E 354 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14245 Z= 0.303 Angle : 0.878 8.793 19445 Z= 0.428 Chirality : 0.051 0.385 2300 Planarity : 0.006 0.049 2360 Dihedral : 13.196 88.632 2745 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.61 % Allowed : 8.52 % Favored : 88.87 % 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: 0.19 (0.19), residues: 1700 helix: 0.60 (0.20), residues: 575 sheet: 0.81 (0.25), residues: 380 loop : -0.54 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.004 0.001 HIS D 125 PHE 0.028 0.002 PHE D 353 TYR 0.019 0.002 TYR C 144 ARG 0.007 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.774 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: A 82 GLN cc_start: 0.6735 (pm20) cc_final: 0.6478 (mp10) REVERT: A 152 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7527 (mm) REVERT: C 152 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7505 (mm) REVERT: D 34 MET cc_start: 0.6918 (tpp) cc_final: 0.6558 (tpp) REVERT: D 100 ASP cc_start: 0.6466 (m-30) cc_final: 0.6147 (m-30) REVERT: D 152 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7636 (mm) REVERT: D 278 THR cc_start: 0.8684 (p) cc_final: 0.7836 (t) REVERT: E 100 ASP cc_start: 0.7097 (m-30) cc_final: 0.6738 (m-30) REVERT: E 152 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7335 (mm) REVERT: E 163 MET cc_start: 0.7673 (pmm) cc_final: 0.7193 (pmm) REVERT: E 278 THR cc_start: 0.8546 (p) cc_final: 0.8054 (t) outliers start: 37 outliers final: 9 residues processed: 220 average time/residue: 0.1973 time to fit residues: 68.7224 Evaluate side-chains 165 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 0.0870 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14245 Z= 0.219 Angle : 0.759 11.253 19445 Z= 0.373 Chirality : 0.044 0.200 2300 Planarity : 0.004 0.044 2360 Dihedral : 10.732 73.278 2745 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.27 % Allowed : 13.66 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.45 (0.19), residues: 1700 helix: 1.06 (0.21), residues: 575 sheet: 0.76 (0.26), residues: 380 loop : -0.50 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.002 0.001 HIS D 125 PHE 0.021 0.002 PHE D 353 TYR 0.024 0.002 TYR C 144 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.697 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: A 34 MET cc_start: 0.6748 (tpp) cc_final: 0.6379 (tpp) REVERT: A 82 GLN cc_start: 0.6682 (pm20) cc_final: 0.6324 (mp10) REVERT: A 152 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (mm) REVERT: C 315 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8318 (tt) REVERT: D 100 ASP cc_start: 0.6512 (m-30) cc_final: 0.6144 (m-30) REVERT: D 152 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7596 (mm) REVERT: D 278 THR cc_start: 0.8601 (p) cc_final: 0.8098 (p) REVERT: E 100 ASP cc_start: 0.6975 (m-30) cc_final: 0.6576 (m-30) REVERT: E 163 MET cc_start: 0.7627 (pmm) cc_final: 0.7407 (pmm) REVERT: E 278 THR cc_start: 0.8542 (p) cc_final: 0.8092 (t) outliers start: 18 outliers final: 9 residues processed: 193 average time/residue: 0.2219 time to fit residues: 66.5289 Evaluate side-chains 162 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14245 Z= 0.196 Angle : 0.753 11.592 19445 Z= 0.363 Chirality : 0.044 0.181 2300 Planarity : 0.004 0.040 2360 Dihedral : 8.588 68.760 2745 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.97 % Allowed : 13.87 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1700 helix: 1.21 (0.21), residues: 570 sheet: 0.57 (0.26), residues: 385 loop : -0.60 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.003 0.001 HIS E 217 PHE 0.018 0.001 PHE E 353 TYR 0.017 0.001 TYR C 144 ARG 0.012 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6818 (tpp) cc_final: 0.6493 (tpp) REVERT: A 82 GLN cc_start: 0.6699 (pm20) cc_final: 0.6256 (mp10) REVERT: A 100 ASP cc_start: 0.6580 (m-30) cc_final: 0.6200 (m-30) REVERT: A 315 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 100 ASP cc_start: 0.6591 (m-30) cc_final: 0.6256 (m-30) REVERT: B 315 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 156 MET cc_start: 0.5578 (ptt) cc_final: 0.5325 (ptt) REVERT: C 243 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6873 (mpp) REVERT: C 315 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8278 (tt) REVERT: D 156 MET cc_start: 0.5213 (ptp) cc_final: 0.4914 (ptp) REVERT: D 278 THR cc_start: 0.8554 (p) cc_final: 0.7933 (t) REVERT: E 34 MET cc_start: 0.7062 (tpp) cc_final: 0.6491 (tpp) REVERT: E 100 ASP cc_start: 0.6787 (m-30) cc_final: 0.6250 (m-30) REVERT: E 152 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7448 (mm) REVERT: E 278 THR cc_start: 0.8500 (p) cc_final: 0.8199 (t) outliers start: 28 outliers final: 14 residues processed: 199 average time/residue: 0.2238 time to fit residues: 68.8701 Evaluate side-chains 173 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 261 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 131 ASN C 217 HIS C 261 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 14245 Z= 0.503 Angle : 0.929 11.776 19445 Z= 0.464 Chirality : 0.049 0.208 2300 Planarity : 0.006 0.065 2360 Dihedral : 9.394 62.206 2745 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.31 % Allowed : 14.23 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1700 helix: 0.89 (0.21), residues: 550 sheet: 0.14 (0.25), residues: 405 loop : -0.18 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 255 HIS 0.009 0.004 HIS D 125 PHE 0.025 0.003 PHE A 64 TYR 0.037 0.003 TYR B 361 ARG 0.007 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6949 (tpp) cc_final: 0.6657 (tpp) REVERT: A 100 ASP cc_start: 0.6563 (m-30) cc_final: 0.6283 (m-30) REVERT: A 315 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 315 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 315 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8331 (tt) REVERT: D 163 MET cc_start: 0.7849 (pmm) cc_final: 0.7583 (mpp) REVERT: D 278 THR cc_start: 0.8759 (p) cc_final: 0.8236 (p) REVERT: D 289 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (t) REVERT: D 315 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8536 (tt) REVERT: E 152 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7616 (mm) REVERT: E 315 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 47 outliers final: 19 residues processed: 191 average time/residue: 0.2173 time to fit residues: 64.7907 Evaluate side-chains 152 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS B 131 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS D 166 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14245 Z= 0.210 Angle : 0.792 11.863 19445 Z= 0.386 Chirality : 0.045 0.215 2300 Planarity : 0.004 0.044 2360 Dihedral : 8.423 62.831 2745 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.18 % Allowed : 16.20 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.46 (0.20), residues: 1700 helix: 1.28 (0.22), residues: 565 sheet: 0.29 (0.25), residues: 395 loop : -0.35 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP D 255 HIS 0.003 0.001 HIS A 125 PHE 0.042 0.002 PHE A 353 TYR 0.016 0.002 TYR A 238 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6549 (m-30) cc_final: 0.6325 (m-30) REVERT: A 150 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 315 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8288 (tt) REVERT: B 78 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8629 (pt) REVERT: B 315 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8449 (tt) REVERT: C 315 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8185 (tt) REVERT: E 100 ASP cc_start: 0.6520 (m-30) cc_final: 0.6075 (m-30) REVERT: E 152 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7516 (mm) REVERT: E 278 THR cc_start: 0.8617 (p) cc_final: 0.7806 (t) outliers start: 31 outliers final: 13 residues processed: 175 average time/residue: 0.2204 time to fit residues: 60.7822 Evaluate side-chains 155 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.0040 chunk 163 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14245 Z= 0.199 Angle : 0.780 15.384 19445 Z= 0.377 Chirality : 0.044 0.206 2300 Planarity : 0.004 0.042 2360 Dihedral : 7.973 61.582 2745 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 16.83 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.51 (0.20), residues: 1700 helix: 1.39 (0.22), residues: 565 sheet: 0.31 (0.26), residues: 395 loop : -0.39 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 255 HIS 0.002 0.001 HIS A 125 PHE 0.035 0.001 PHE A 353 TYR 0.016 0.001 TYR A 238 ARG 0.004 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6544 (m-30) cc_final: 0.6291 (m-30) REVERT: A 150 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 315 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8226 (tt) REVERT: B 78 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8662 (pt) REVERT: B 163 MET cc_start: 0.7723 (pmm) cc_final: 0.6819 (mpp) REVERT: B 315 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (tt) REVERT: C 244 TYR cc_start: 0.7316 (m-80) cc_final: 0.6893 (m-80) REVERT: C 302 TRP cc_start: 0.8049 (t-100) cc_final: 0.7728 (t-100) REVERT: C 315 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8161 (tt) REVERT: D 72 MET cc_start: 0.7222 (tpp) cc_final: 0.7007 (tpp) REVERT: D 315 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8455 (tt) REVERT: E 34 MET cc_start: 0.6846 (tpp) cc_final: 0.6633 (tpp) REVERT: E 100 ASP cc_start: 0.6372 (m-30) cc_final: 0.5902 (m-30) REVERT: E 152 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7520 (mm) REVERT: E 278 THR cc_start: 0.8681 (p) cc_final: 0.8272 (t) outliers start: 29 outliers final: 15 residues processed: 173 average time/residue: 0.2170 time to fit residues: 59.4380 Evaluate side-chains 163 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 0.0030 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14245 Z= 0.235 Angle : 0.791 14.604 19445 Z= 0.382 Chirality : 0.045 0.371 2300 Planarity : 0.004 0.043 2360 Dihedral : 7.879 59.918 2745 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 17.61 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.59 (0.21), residues: 1700 helix: 1.44 (0.22), residues: 565 sheet: 0.32 (0.26), residues: 395 loop : -0.31 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 255 HIS 0.002 0.001 HIS A 125 PHE 0.033 0.001 PHE A 353 TYR 0.030 0.002 TYR C 239 ARG 0.004 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6581 (m-30) cc_final: 0.6337 (m-30) REVERT: A 150 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 315 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 78 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8685 (pt) REVERT: B 163 MET cc_start: 0.7738 (pmm) cc_final: 0.6893 (mpp) REVERT: B 315 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (tt) REVERT: C 315 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8183 (tt) REVERT: D 34 MET cc_start: 0.6969 (tpp) cc_final: 0.6713 (tpp) REVERT: D 72 MET cc_start: 0.7300 (tpp) cc_final: 0.7090 (tpp) REVERT: D 315 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8432 (tt) REVERT: E 100 ASP cc_start: 0.6510 (m-30) cc_final: 0.6069 (m-30) REVERT: E 152 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7512 (mm) REVERT: E 315 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8365 (tt) outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 0.2141 time to fit residues: 54.9491 Evaluate side-chains 157 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 0.0670 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14245 Z= 0.342 Angle : 0.843 14.226 19445 Z= 0.412 Chirality : 0.046 0.312 2300 Planarity : 0.005 0.051 2360 Dihedral : 8.220 57.838 2745 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.11 % Allowed : 17.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1700 helix: 1.15 (0.22), residues: 575 sheet: 0.25 (0.26), residues: 390 loop : -0.46 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 255 HIS 0.005 0.002 HIS A 125 PHE 0.031 0.002 PHE A 353 TYR 0.031 0.003 TYR C 238 ARG 0.005 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6629 (m-30) cc_final: 0.6198 (m-30) REVERT: A 150 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 179 MET cc_start: 0.6978 (mmp) cc_final: 0.6602 (mmp) REVERT: A 249 LEU cc_start: 0.9010 (tp) cc_final: 0.8724 (tt) REVERT: A 315 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8332 (tt) REVERT: B 315 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8460 (tt) REVERT: C 315 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8201 (tt) REVERT: D 315 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8480 (tt) REVERT: E 100 ASP cc_start: 0.6461 (m-30) cc_final: 0.5964 (m-30) REVERT: E 152 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (mm) REVERT: E 315 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.2018 time to fit residues: 51.9711 Evaluate side-chains 158 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 14245 Z= 0.214 Angle : 0.841 17.202 19445 Z= 0.397 Chirality : 0.045 0.261 2300 Planarity : 0.004 0.044 2360 Dihedral : 7.751 59.064 2745 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.69 % Allowed : 19.01 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.48 (0.21), residues: 1700 helix: 1.33 (0.22), residues: 575 sheet: 0.34 (0.26), residues: 395 loop : -0.43 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 255 HIS 0.002 0.001 HIS A 125 PHE 0.030 0.001 PHE A 353 TYR 0.022 0.002 TYR C 238 ARG 0.005 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.524 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: A 100 ASP cc_start: 0.6460 (m-30) cc_final: 0.6200 (m-30) REVERT: A 150 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 179 MET cc_start: 0.6829 (mmp) cc_final: 0.6492 (mmp) REVERT: A 315 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 163 MET cc_start: 0.7718 (pmm) cc_final: 0.6917 (mpp) REVERT: B 244 TYR cc_start: 0.7261 (m-80) cc_final: 0.6880 (m-80) REVERT: B 315 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8492 (tt) REVERT: C 34 MET cc_start: 0.6819 (tpt) cc_final: 0.6292 (tpp) REVERT: C 315 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8151 (tt) REVERT: D 34 MET cc_start: 0.6703 (tpp) cc_final: 0.6392 (tpp) REVERT: D 72 MET cc_start: 0.7414 (tpp) cc_final: 0.7085 (tpp) REVERT: D 185 GLU cc_start: 0.7501 (pm20) cc_final: 0.7170 (pm20) REVERT: D 315 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8420 (tt) REVERT: E 100 ASP cc_start: 0.6383 (m-30) cc_final: 0.5985 (m-30) REVERT: E 152 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7439 (mm) REVERT: E 315 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8337 (tt) outliers start: 24 outliers final: 15 residues processed: 164 average time/residue: 0.2032 time to fit residues: 52.9955 Evaluate side-chains 154 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 0.0470 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.031390 restraints weight = 96316.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.032548 restraints weight = 55469.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033379 restraints weight = 37033.803| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14245 Z= 0.228 Angle : 0.830 13.694 19445 Z= 0.397 Chirality : 0.044 0.253 2300 Planarity : 0.004 0.045 2360 Dihedral : 7.635 57.719 2745 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 19.01 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.50 (0.21), residues: 1700 helix: 1.34 (0.22), residues: 575 sheet: 0.39 (0.26), residues: 395 loop : -0.43 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 255 HIS 0.004 0.001 HIS A 125 PHE 0.029 0.001 PHE A 353 TYR 0.022 0.002 TYR C 238 ARG 0.004 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.78 seconds wall clock time: 44 minutes 26.64 seconds (2666.64 seconds total)