Starting phenix.real_space_refine on Fri Aug 9 22:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/08_2024/8bhb_16051_trim.cif" } resolution = 2.54 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= 0.001 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8910 2.51 5 N 2290 2.21 5 O 2550 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27250 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 15.10, per 1000 atoms: 0.55 Number of scatterers: 27250 At special positions: 0 Unit cell: (90.628, 93.888, 123.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2550 8.00 N 2290 7.00 C 8910 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 22.40 Conformation dependent library (CDL) restraints added in 3.0 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.4% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.576A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.574A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 4.148A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 4.034A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.613A pdb=" N ILE A 124 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 112 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG A 135 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE B 124 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER B 139 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 110 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 137 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 112 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG B 135 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE C 124 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 129 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA C 112 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG C 135 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.613A pdb=" N ILE D 124 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG D 129 " --> pdb=" O TRP D 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA D 112 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG D 135 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE E 124 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG E 129 " --> pdb=" O TRP E 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA E 112 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG E 135 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2430 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: 11.01 Time building geometry restraints manager: 22.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 18 1.23 - 1.42: 6102 1.42 - 1.62: 7870 1.62 - 1.81: 150 Bond restraints: 27555 Sorted by residual: bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 27550 not shown) Histogram of bond angle deviations from ideal: 100.34 - 114.23: 33060 114.23 - 128.13: 16295 128.13 - 142.02: 160 142.02 - 155.92: 0 155.92 - 169.81: 5 Bond angle restraints: 49520 Sorted by residual: angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 126.91 -5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.26e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 126.85 -5.15 1.80e+00 3.09e-01 8.20e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 126.83 -5.13 1.80e+00 3.09e-01 8.12e+00 ... (remaining 49515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 12603 15.91 - 31.82: 382 31.82 - 47.73: 90 47.73 - 63.63: 95 63.63 - 79.54: 5 Dihedral angle restraints: 13175 sinusoidal: 7045 harmonic: 6130 Sorted by residual: dihedral pdb=" CB MET E 115 " pdb=" CG MET E 115 " pdb=" SD MET E 115 " pdb=" CE MET E 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.42 -43.42 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET D 115 " pdb=" CG MET D 115 " pdb=" SD MET D 115 " pdb=" CE MET D 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.41 -43.41 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " pdb=" CE MET A 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.40 -43.40 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1225 0.024 - 0.047: 607 0.047 - 0.071: 173 0.071 - 0.095: 71 0.095 - 0.119: 84 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EIE E 502 " 0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE E 502 " 0.364 2.00e-02 2.50e+03 pdb=" C12 EIE E 502 " 0.062 2.00e-02 2.50e+03 pdb=" C13 EIE E 502 " -0.130 2.00e-02 2.50e+03 pdb=" C7 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" C8 EIE E 502 " -0.015 2.00e-02 2.50e+03 pdb=" C9 EIE E 502 " 0.294 2.00e-02 2.50e+03 pdb=" N1 EIE E 502 " 0.787 2.00e-02 2.50e+03 pdb=" N2 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" N3 EIE E 502 " -0.978 2.00e-02 2.50e+03 pdb=" N4 EIE E 502 " -0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE D 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE D 502 " -0.364 2.00e-02 2.50e+03 pdb=" C12 EIE D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE D 502 " 0.131 2.00e-02 2.50e+03 pdb=" C7 EIE D 502 " 0.210 2.00e-02 2.50e+03 pdb=" C8 EIE D 502 " 0.014 2.00e-02 2.50e+03 pdb=" C9 EIE D 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE D 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE D 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE D 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE D 502 " 0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE B 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.83e+03 pdb=" C11 EIE B 502 " -0.365 2.00e-02 2.50e+03 pdb=" C12 EIE B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE B 502 " 0.130 2.00e-02 2.50e+03 pdb=" C7 EIE B 502 " 0.209 2.00e-02 2.50e+03 pdb=" C8 EIE B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C9 EIE B 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE B 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE B 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE B 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE B 502 " 0.445 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2393 2.25 - 2.83: 62032 2.83 - 3.42: 69894 3.42 - 4.01: 100558 4.01 - 4.60: 155147 Nonbonded interactions: 390024 Sorted by model distance: nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.657 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.657 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.658 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.658 2.450 nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.658 2.450 ... (remaining 390019 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' } 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 individual isotropic 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: 15.840 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: 0.440 Extract box with map and model: 0.970 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 90.870 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 : 0.003 0.050 14140 Z= 0.174 Angle : 0.415 6.270 19245 Z= 0.193 Chirality : 0.037 0.119 2160 Planarity : 0.021 0.461 2395 Dihedral : 7.198 79.543 5165 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.13 (0.21), residues: 1670 helix: 2.96 (0.22), residues: 585 sheet: 0.65 (0.27), residues: 435 loop : 0.61 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 414 HIS 0.003 0.001 HIS B 195 PHE 0.005 0.001 PHE E 104 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.380 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 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8284 (tptp) REVERT: A 193 GLN cc_start: 0.8146 (pt0) cc_final: 0.7829 (pm20) REVERT: B 109 LYS cc_start: 0.8583 (tttt) cc_final: 0.8245 (tptp) REVERT: B 193 GLN cc_start: 0.8164 (pt0) cc_final: 0.7957 (pm20) REVERT: B 253 GLU cc_start: 0.8677 (pm20) cc_final: 0.7852 (pm20) REVERT: C 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8272 (tptp) REVERT: D 109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8304 (tptp) REVERT: D 193 GLN cc_start: 0.8169 (pt0) cc_final: 0.7950 (pm20) REVERT: E 109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8289 (tptp) REVERT: E 193 GLN cc_start: 0.8149 (pt0) cc_final: 0.7898 (pm20) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 3.1798 time to fit residues: 911.3376 Evaluate side-chains 135 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN C 155 ASN D 155 ASN E 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14140 Z= 0.204 Angle : 0.489 6.907 19245 Z= 0.261 Chirality : 0.040 0.133 2160 Planarity : 0.004 0.032 2395 Dihedral : 3.507 18.159 2030 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 7.11 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.15 (0.21), residues: 1670 helix: 3.20 (0.20), residues: 615 sheet: 0.50 (0.25), residues: 455 loop : 0.36 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 73 HIS 0.002 0.001 HIS C 221 PHE 0.010 0.001 PHE C 68 TYR 0.008 0.001 TYR E 194 ARG 0.003 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8271 (tptp) REVERT: A 193 GLN cc_start: 0.8271 (pt0) cc_final: 0.7914 (pm20) REVERT: A 277 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7753 (mmt180) REVERT: B 109 LYS cc_start: 0.8581 (tttt) cc_final: 0.8250 (tptp) REVERT: B 115 MET cc_start: 0.8498 (mmp) cc_final: 0.7969 (mmp) REVERT: B 193 GLN cc_start: 0.8302 (pt0) cc_final: 0.8033 (pm20) REVERT: B 251 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7369 (t0) REVERT: C 109 LYS cc_start: 0.8571 (tttt) cc_final: 0.8232 (tptp) REVERT: D 109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8275 (tptp) REVERT: D 193 GLN cc_start: 0.8297 (pt0) cc_final: 0.8013 (pm20) REVERT: D 251 ASN cc_start: 0.8070 (t0) cc_final: 0.7772 (t0) REVERT: E 109 LYS cc_start: 0.8594 (tttt) cc_final: 0.8280 (tptp) REVERT: E 193 GLN cc_start: 0.8262 (pt0) cc_final: 0.7997 (pm20) outliers start: 21 outliers final: 9 residues processed: 163 average time/residue: 2.5304 time to fit residues: 456.7238 Evaluate side-chains 149 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 0.0980 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14140 Z= 0.250 Angle : 0.485 6.695 19245 Z= 0.256 Chirality : 0.041 0.130 2160 Planarity : 0.004 0.038 2395 Dihedral : 3.900 18.679 2030 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 7.72 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.97 (0.21), residues: 1670 helix: 3.23 (0.20), residues: 610 sheet: 0.27 (0.24), residues: 455 loop : 0.19 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 291 HIS 0.004 0.001 HIS D 221 PHE 0.013 0.002 PHE C 69 TYR 0.012 0.001 TYR E 132 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 109 LYS cc_start: 0.8598 (tttt) cc_final: 0.8242 (tptp) REVERT: A 193 GLN cc_start: 0.8310 (pt0) cc_final: 0.7990 (pm20) REVERT: A 277 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7782 (mmt180) REVERT: B 109 LYS cc_start: 0.8563 (tttt) cc_final: 0.8208 (tptp) REVERT: B 193 GLN cc_start: 0.8306 (pt0) cc_final: 0.8036 (pm20) REVERT: B 251 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7351 (t0) REVERT: C 23 ASP cc_start: 0.8609 (m-30) cc_final: 0.8397 (m-30) REVERT: C 109 LYS cc_start: 0.8567 (tttt) cc_final: 0.8224 (tptp) REVERT: D 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8221 (tptp) REVERT: D 193 GLN cc_start: 0.8349 (pt0) cc_final: 0.8024 (pm20) REVERT: D 251 ASN cc_start: 0.8098 (t0) cc_final: 0.7805 (t0) REVERT: E 109 LYS cc_start: 0.8581 (tttt) cc_final: 0.8240 (tptp) REVERT: E 193 GLN cc_start: 0.8298 (pt0) cc_final: 0.7998 (pm20) outliers start: 26 outliers final: 10 residues processed: 151 average time/residue: 2.4082 time to fit residues: 405.0860 Evaluate side-chains 143 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14140 Z= 0.262 Angle : 0.479 6.711 19245 Z= 0.252 Chirality : 0.040 0.126 2160 Planarity : 0.004 0.038 2395 Dihedral : 3.986 19.545 2030 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.42 % Allowed : 7.32 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.92 (0.21), residues: 1670 helix: 3.28 (0.20), residues: 610 sheet: 0.18 (0.24), residues: 455 loop : 0.09 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 73 HIS 0.003 0.001 HIS C 221 PHE 0.011 0.002 PHE B 69 TYR 0.010 0.001 TYR E 132 ARG 0.002 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8236 (tptp) REVERT: A 193 GLN cc_start: 0.8320 (pt0) cc_final: 0.7995 (pm20) REVERT: B 109 LYS cc_start: 0.8567 (tttt) cc_final: 0.8207 (tptp) REVERT: B 134 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8982 (pt) REVERT: B 193 GLN cc_start: 0.8322 (pt0) cc_final: 0.8052 (pm20) REVERT: B 251 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7372 (t0) REVERT: C 109 LYS cc_start: 0.8593 (tttt) cc_final: 0.8227 (tptp) REVERT: D 109 LYS cc_start: 0.8602 (tttt) cc_final: 0.8221 (tptp) REVERT: D 193 GLN cc_start: 0.8370 (pt0) cc_final: 0.8004 (pm20) REVERT: D 251 ASN cc_start: 0.8105 (t0) cc_final: 0.7811 (t0) REVERT: E 109 LYS cc_start: 0.8593 (tttt) cc_final: 0.8226 (tptp) REVERT: E 193 GLN cc_start: 0.8303 (pt0) cc_final: 0.8002 (pm20) outliers start: 36 outliers final: 15 residues processed: 155 average time/residue: 2.2024 time to fit residues: 380.3679 Evaluate side-chains 152 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.0020 chunk 40 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: