Starting phenix.real_space_refine on Mon Aug 25 10:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bho_16063/08_2025/8bho_16063.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 8925 2.51 5 N 2275 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 10 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.16 Number of scatterers: 27190 At special positions: 0 Unit cell: (92.4, 94.5, 123.9, 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 2490 8.00 N 2275 7.00 C 8925 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 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: 2.11 Conformation dependent library (CDL) restraints added in 814.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 45 helices and 15 sheets defined 39.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.672A 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 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: 3.859A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.521A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.959A 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: 3.673A 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 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: 3.858A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.521A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.673A 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 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: 3.859A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.521A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.673A 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 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: 3.859A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.521A pdb=" N ALA D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.672A 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 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: 3.858A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.521A pdb=" N ALA E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.959A 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 107 through 112 removed outlier: 6.735A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.675A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A 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: 4.674A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR B 133 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A 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: 4.675A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A 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: 4.675A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A 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: 4.675A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.734A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A 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: 4.674A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2355 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: 6.17 Time building geometry restraints manager: 3.09 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: 10 1.23 - 1.42: 6105 1.42 - 1.61: 7885 1.61 - 1.81: 150 Bond restraints: 27565 Sorted by residual: 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 2.52e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+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 2.50e+01 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 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 49291 1.72 - 3.44: 190 3.44 - 5.16: 39 5.16 - 6.87: 5 6.87 - 8.59: 15 Bond angle restraints: 49540 Sorted by residual: angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 9.98e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.93e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.82e+00 ... (remaining 49535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 12611 14.62 - 29.25: 374 29.25 - 43.87: 130 43.87 - 58.49: 105 58.49 - 73.12: 15 Dihedral angle restraints: 13235 sinusoidal: 7105 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS D 315 " pdb=" CG LYS D 315 " pdb=" CD LYS D 315 " pdb=" CE LYS D 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.65 -40.65 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS C 315 " pdb=" CG LYS C 315 " pdb=" CD LYS C 315 " pdb=" CE LYS C 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 ... (remaining 13232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1889 0.055 - 0.111: 256 0.111 - 0.166: 15 0.166 - 0.221: 0 0.221 - 0.277: 5 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C13 QMJ D 502 " pdb=" C14 QMJ D 502 " pdb=" C4 QMJ D 502 " pdb=" N2 QMJ D 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 QMJ C 502 " pdb=" C14 QMJ C 502 " pdb=" C4 QMJ C 502 " pdb=" N2 QMJ C 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C13 QMJ A 502 " pdb=" C14 QMJ A 502 " pdb=" C4 QMJ A 502 " pdb=" N2 QMJ A 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2162 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QMJ A 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ A 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ A 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ A 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ A 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ A 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ E 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ E 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ E 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ E 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ E 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ C 502 " -0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ C 502 " 0.031 2.00e-02 2.50e+03 pdb=" C13 QMJ C 502 " 0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ C 502 " -0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ C 502 " -0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ C 502 " 0.375 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 5486 2.31 - 2.88: 62144 2.88 - 3.45: 67787 3.45 - 4.03: 97104 4.03 - 4.60: 146582 Nonbonded interactions: 379103 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.735 2.450 ... (remaining 379098 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: 0.05 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: 2.830 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: 0.180 Extract box with map and model: 0.260 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.380 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.002 0.035 14160 Z= 0.081 Angle : 0.446 8.592 19290 Z= 0.193 Chirality : 0.039 0.277 2165 Planarity : 0.014 0.301 2395 Dihedral : 7.455 73.117 5225 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.22), residues: 1670 helix: 3.34 (0.21), residues: 575 sheet: 0.79 (0.27), residues: 435 loop : 0.89 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 34 TYR 0.004 0.001 TYR C 285 PHE 0.004 0.000 PHE C 149 TRP 0.002 0.000 TRP C 73 HIS 0.002 0.000 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00170 (14150) covalent geometry : angle 0.44487 (19265) SS BOND : bond 0.00050 ( 5) SS BOND : angle 0.22623 ( 10) hydrogen bonds : bond 0.23740 ( 710) hydrogen bonds : angle 7.59655 ( 2355) link_NAG-ASN : bond 0.00031 ( 5) link_NAG-ASN : angle 1.37233 ( 15) *********************** 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 160 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8782 (ttm) cc_final: 0.8433 (ttm) REVERT: B 48 MET cc_start: 0.8877 (ttm) cc_final: 0.8649 (mtp) REVERT: B 289 MET cc_start: 0.8636 (ttp) cc_final: 0.8315 (ttp) REVERT: D 289 MET cc_start: 0.8606 (ttp) cc_final: 0.8395 (ttp) REVERT: E 289 MET cc_start: 0.8619 (ttp) cc_final: 0.8387 (ttp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.3472 time to fit residues: 234.5448 Evaluate side-chains 106 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 71 GLN B 85 GLN C 71 GLN D 71 GLN D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063762 restraints weight = 97052.295| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.04 r_work: 0.2969 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14160 Z= 0.296 Angle : 0.627 4.733 19290 Z= 0.336 Chirality : 0.043 0.147 2165 Planarity : 0.006 0.099 2395 Dihedral : 5.834 62.261 2090 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.01 % Allowed : 4.90 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.21), residues: 1670 helix: 3.02 (0.21), residues: 580 sheet: -0.07 (0.24), residues: 510 loop : 0.28 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 190 TYR 0.013 0.002 TYR D 163 PHE 0.013 0.002 PHE B 149 TRP 0.010 0.002 TRP C 73 HIS 0.006 0.001 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00668 (14150) covalent geometry : angle 0.62608 (19265) SS BOND : bond 0.00618 ( 5) SS BOND : angle 0.56433 ( 10) hydrogen bonds : bond 0.04810 ( 710) hydrogen bonds : angle 4.90541 ( 2355) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.14425 ( 15) *********************** 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 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.456 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 239 MET cc_start: 0.9059 (mmm) cc_final: 0.8725 (mmm) REVERT: A 245 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: D 301 PHE cc_start: 0.8534 (t80) cc_final: 0.8319 (t80) REVERT: D 397 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8224 (ttt) REVERT: E 397 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7897 (ttp) outliers start: 15 outliers final: 1 residues processed: 113 average time/residue: 1.0981 time to fit residues: 136.3678 Evaluate side-chains 94 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 167 ASN 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 56 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064347 restraints weight = 96088.646| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.00 r_work: 0.2996 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14160 Z= 0.142 Angle : 0.479 5.159 19290 Z= 0.254 Chirality : 0.039 0.142 2165 Planarity : 0.005 0.068 2395 Dihedral : 4.043 36.687 2090 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.60 % Allowed : 6.64 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.21), residues: 1670 helix: 3.24 (0.21), residues: 580 sheet: 0.01 (0.25), residues: 435 loop : 0.05 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.007 0.001 TYR A 417 PHE 0.009 0.001 PHE A 261 TRP 0.008 0.001 TRP C 73 HIS 0.002 0.000 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00305 (14150) covalent geometry : angle 0.47833 (19265) SS BOND : bond 0.00392 ( 5) SS BOND : angle 0.59456 ( 10) hydrogen bonds : bond 0.04359 ( 710) hydrogen bonds : angle 4.55674 ( 2355) link_NAG-ASN : bond 0.00043 ( 5) link_NAG-ASN : angle 1.11302 ( 15) *********************** 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 110 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.569 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: A 239 MET cc_start: 0.9057 (mmm) cc_final: 0.8853 (mmm) REVERT: C 245 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: D 301 PHE cc_start: 0.8477 (t80) cc_final: 0.8232 (t80) REVERT: D 397 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (ttt) REVERT: E 397 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7965 (ttp) outliers start: 9 outliers final: 1 residues processed: 102 average time/residue: 1.2024 time to fit residues: 135.0133 Evaluate side-chains 96 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 397 MET 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 113 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063357 restraints weight = 96083.108| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.04 r_work: 0.2980 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14160 Z= 0.170 Angle : 0.483 5.336 19290 Z= 0.256 Chirality : 0.040 0.139 2165 Planarity : 0.005 0.067 2395 Dihedral : 3.722 25.629 2090 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.74 % Allowed : 6.17 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1670 helix: 3.34 (0.21), residues: 550 sheet: -0.09 (0.24), residues: 455 loop : 0.04 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.009 0.001 TYR A 417 PHE 0.010 0.001 PHE D 104 TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00373 (14150) covalent geometry : angle 0.48134 (19265) SS BOND : bond 0.00419 ( 5) SS BOND : angle 0.78140 ( 10) hydrogen bonds : bond 0.03880 ( 710) hydrogen bonds : angle 4.34593 ( 2355) link_NAG-ASN : bond 0.00137 ( 5) link_NAG-ASN : angle 1.20309 ( 15) *********************** 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 111 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: B 239 MET cc_start: 0.9177 (mmm) cc_final: 0.8932 (mmm) REVERT: C 245 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: C 306 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: D 301 PHE cc_start: 0.8499 (t80) cc_final: 0.8244 (t80) REVERT: D 397 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8238 (ttt) outliers start: 11 outliers final: 2 residues processed: 104 average time/residue: 1.1636 time to fit residues: 133.2921 Evaluate side-chains 104 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063820 restraints weight = 96161.653| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.00 r_work: 0.2995 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14160 Z= 0.138 Angle : 0.456 5.404 19290 Z= 0.240 Chirality : 0.039 0.137 2165 Planarity : 0.004 0.061 2395 Dihedral : 3.688 20.642 2090 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.74 % Allowed : 6.11 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.21), residues: 1670 helix: 3.45 (0.21), residues: 580 sheet: -0.10 (0.25), residues: 430 loop : -0.04 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.008 0.001 TYR E 417 PHE 0.009 0.001 PHE A 261 TRP 0.010 0.001 TRP A 114 HIS 0.002 0.000 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00299 (14150) covalent geometry : angle 0.45440 (19265) SS BOND : bond 0.00357 ( 5) SS BOND : angle 0.72654 ( 10) hydrogen bonds : bond 0.03592 ( 710) hydrogen bonds : angle 4.18892 ( 2355) link_NAG-ASN : bond 0.00084 ( 5) link_NAG-ASN : angle 1.16676 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 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 113 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.525 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 245 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: B 306 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: C 245 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: D 301 PHE cc_start: 0.8497 (t80) cc_final: 0.8250 (t80) REVERT: D 397 MET cc_start: 0.8493 (ttm) cc_final: 0.8213 (ttt) REVERT: E 27 ASP cc_start: 0.7194 (p0) cc_final: 0.6929 (p0) REVERT: E 120 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8204 (mtt90) REVERT: E 397 MET cc_start: 0.8383 (ttm) cc_final: 0.7949 (ttp) outliers start: 11 outliers final: 1 residues processed: 108 average time/residue: 1.1294 time to fit residues: 134.7279 Evaluate side-chains 98 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062403 restraints weight = 96334.163| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.11 r_work: 0.2908 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14160 Z= 0.223 Angle : 0.502 5.479 19290 Z= 0.266 Chirality : 0.040 0.134 2165 Planarity : 0.005 0.055 2395 Dihedral : 4.077 26.265 2090 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.81 % Allowed : 6.38 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.21), residues: 1670 helix: 3.52 (0.21), residues: 550 sheet: -0.26 (0.24), residues: 455 loop : -0.08 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 190 TYR 0.012 0.001 TYR D 417 PHE 0.012 0.001 PHE B 104 TRP 0.015 0.001 TRP A 114 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00494 (14150) covalent geometry : angle 0.50061 (19265) SS BOND : bond 0.00441 ( 5) SS BOND : angle 0.91988 ( 10) hydrogen bonds : bond 0.03849 ( 710) hydrogen bonds : angle 4.27198 ( 2355) link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 1.32747 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 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 112 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: B 306 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: C 144 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: C 245 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: C 306 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: D 120 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8398 (mtp85) REVERT: D 301 PHE cc_start: 0.8402 (t80) cc_final: 0.8124 (t80) REVERT: D 397 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8140 (ttt) REVERT: E 27 ASP cc_start: 0.7307 (p0) cc_final: 0.7080 (p0) REVERT: E 397 MET cc_start: 0.8298 (ttm) cc_final: 0.7881 (ttp) outliers start: 12 outliers final: 1 residues processed: 105 average time/residue: 1.1779 time to fit residues: 136.0291 Evaluate side-chains 102 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.075076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061511 restraints weight = 96641.212| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.10 r_work: 0.2887 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14160 Z= 0.265 Angle : 0.532 5.631 19290 Z= 0.284 Chirality : 0.041 0.139 2165 Planarity : 0.005 0.061 2395 Dihedral : 4.434 33.962 2090 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.87 % Allowed : 6.85 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.21), residues: 1670 helix: 3.43 (0.21), residues: 550 sheet: -0.44 (0.24), residues: 455 loop : -0.19 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.015 0.001 TYR A 417 PHE 0.014 0.002 PHE D 104 TRP 0.017 0.001 TRP A 114 HIS 0.003 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00586 (14150) covalent geometry : angle 0.53066 (19265) SS BOND : bond 0.00501 ( 5) SS BOND : angle 0.96282 ( 10) hydrogen bonds : bond 0.04025 ( 710) hydrogen bonds : angle 4.36680 ( 2355) link_NAG-ASN : bond 0.00378 ( 5) link_NAG-ASN : angle 1.50171 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 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 110 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7373 (p0) cc_final: 0.7069 (p0) REVERT: A 115 MET cc_start: 0.8189 (mmt) cc_final: 0.7954 (mmt) REVERT: A 245 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: A 306 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8431 (tm-30) REVERT: B 27 ASP cc_start: 0.7645 (p0) cc_final: 0.7354 (p0) REVERT: B 61 MET cc_start: 0.8988 (mtp) cc_final: 0.8771 (mmt) REVERT: B 115 MET cc_start: 0.8274 (mmt) cc_final: 0.7927 (mmt) REVERT: B 306 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: C 84 MET cc_start: 0.6660 (ttm) cc_final: 0.6397 (ttm) REVERT: C 144 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8206 (mtt) REVERT: C 245 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: C 306 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: D 61 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8648 (mmm) REVERT: D 301 PHE cc_start: 0.8420 (t80) cc_final: 0.8142 (t80) REVERT: D 397 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8150 (ttt) REVERT: E 27 ASP cc_start: 0.7385 (p0) cc_final: 0.7085 (p0) REVERT: E 397 MET cc_start: 0.8307 (ttm) cc_final: 0.7923 (ttp) outliers start: 13 outliers final: 2 residues processed: 101 average time/residue: 1.1284 time to fit residues: 126.1026 Evaluate side-chains 102 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063107 restraints weight = 96181.954| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.10 r_work: 0.2925 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14160 Z= 0.148 Angle : 0.468 5.850 19290 Z= 0.246 Chirality : 0.039 0.139 2165 Planarity : 0.004 0.061 2395 Dihedral : 4.034 23.801 2090 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.67 % Allowed : 7.05 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1670 helix: 3.66 (0.21), residues: 550 sheet: -0.33 (0.25), residues: 430 loop : -0.16 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 190 TYR 0.009 0.001 TYR A 417 PHE 0.009 0.001 PHE D 104 TRP 0.019 0.001 TRP A 114 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00324 (14150) covalent geometry : angle 0.46704 (19265) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.84344 ( 10) hydrogen bonds : bond 0.03567 ( 710) hydrogen bonds : angle 4.18532 ( 2355) link_NAG-ASN : bond 0.00083 ( 5) link_NAG-ASN : angle 1.26343 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 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 108 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7315 (p0) cc_final: 0.6964 (p0) REVERT: A 115 MET cc_start: 0.8140 (mmt) cc_final: 0.7872 (mmt) REVERT: A 197 MET cc_start: 0.8280 (mmp) cc_final: 0.7950 (mtm) REVERT: A 245 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: A 306 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: B 27 ASP cc_start: 0.7579 (p0) cc_final: 0.7287 (p0) REVERT: B 115 MET cc_start: 0.8230 (mmt) cc_final: 0.7982 (mmt) REVERT: B 120 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8270 (mtt90) REVERT: B 306 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: C 84 MET cc_start: 0.6581 (ttm) cc_final: 0.6358 (ttm) REVERT: C 245 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: D 301 PHE cc_start: 0.8390 (t80) cc_final: 0.8099 (t80) REVERT: D 397 MET cc_start: 0.8396 (ttm) cc_final: 0.8129 (ttt) REVERT: E 27 ASP cc_start: 0.7387 (p0) cc_final: 0.7105 (p0) REVERT: E 120 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8247 (mtt90) REVERT: E 397 MET cc_start: 0.8284 (ttm) cc_final: 0.7869 (ttp) outliers start: 10 outliers final: 2 residues processed: 103 average time/residue: 1.0920 time to fit residues: 124.3570 Evaluate side-chains 100 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063246 restraints weight = 96427.713| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.08 r_work: 0.2904 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14160 Z= 0.212 Angle : 0.500 5.878 19290 Z= 0.264 Chirality : 0.040 0.136 2165 Planarity : 0.004 0.074 2395 Dihedral : 4.204 28.521 2090 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.60 % Allowed : 7.25 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.21), residues: 1670 helix: 3.60 (0.21), residues: 550 sheet: -0.39 (0.25), residues: 430 loop : -0.24 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.013 0.001 TYR D 417 PHE 0.013 0.001 PHE C 104 TRP 0.020 0.001 TRP A 114 HIS 0.002 0.001 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00468 (14150) covalent geometry : angle 0.49812 (19265) SS BOND : bond 0.00443 ( 5) SS BOND : angle 0.97239 ( 10) hydrogen bonds : bond 0.03746 ( 710) hydrogen bonds : angle 4.23587 ( 2355) link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 1.36766 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 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 103 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7223 (p0) cc_final: 0.6880 (p0) REVERT: A 115 MET cc_start: 0.8225 (mmt) cc_final: 0.7899 (mmt) REVERT: A 197 MET cc_start: 0.8238 (mmp) cc_final: 0.7891 (mtm) REVERT: A 245 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: A 306 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: B 27 ASP cc_start: 0.7598 (p0) cc_final: 0.7315 (p0) REVERT: B 115 MET cc_start: 0.8230 (mmt) cc_final: 0.8020 (mmt) REVERT: B 120 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8290 (mtt90) REVERT: B 306 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: C 84 MET cc_start: 0.6633 (ttm) cc_final: 0.6397 (ttm) REVERT: C 144 MET cc_start: 0.8439 (mtm) cc_final: 0.8156 (mtt) REVERT: C 245 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: D 301 PHE cc_start: 0.8400 (t80) cc_final: 0.8116 (t80) REVERT: D 397 MET cc_start: 0.8409 (ttm) cc_final: 0.8149 (ttt) REVERT: E 27 ASP cc_start: 0.7419 (p0) cc_final: 0.7187 (p0) REVERT: E 120 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8263 (mtt90) REVERT: E 397 MET cc_start: 0.8304 (ttm) cc_final: 0.7908 (ttp) outliers start: 9 outliers final: 2 residues processed: 97 average time/residue: 1.1027 time to fit residues: 118.6031 Evaluate side-chains 99 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063356 restraints weight = 95835.634| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.07 r_work: 0.2929 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14160 Z= 0.144 Angle : 0.463 6.375 19290 Z= 0.243 Chirality : 0.039 0.138 2165 Planarity : 0.004 0.084 2395 Dihedral : 3.953 22.024 2090 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.54 % Allowed : 7.32 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.21), residues: 1670 helix: 3.73 (0.21), residues: 550 sheet: -0.34 (0.25), residues: 430 loop : -0.18 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.008 0.001 TYR D 417 PHE 0.009 0.001 PHE D 104 TRP 0.023 0.001 TRP A 114 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00315 (14150) covalent geometry : angle 0.46132 (19265) SS BOND : bond 0.00387 ( 5) SS BOND : angle 0.85324 ( 10) hydrogen bonds : bond 0.03455 ( 710) hydrogen bonds : angle 4.12090 ( 2355) link_NAG-ASN : bond 0.00094 ( 5) link_NAG-ASN : angle 1.26223 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 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 103 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.628 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 27 ASP cc_start: 0.7229 (p0) cc_final: 0.6854 (p0) REVERT: A 115 MET cc_start: 0.8159 (mmt) cc_final: 0.7845 (mmt) REVERT: A 197 MET cc_start: 0.8213 (mmp) cc_final: 0.7850 (mtm) REVERT: A 245 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: A 306 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: B 27 ASP cc_start: 0.7579 (p0) cc_final: 0.7284 (p0) REVERT: B 61 MET cc_start: 0.9021 (mmt) cc_final: 0.8631 (mmp) REVERT: B 120 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8277 (mtt90) REVERT: B 306 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: C 84 MET cc_start: 0.6621 (ttm) cc_final: 0.6377 (ttm) REVERT: C 144 MET cc_start: 0.8414 (mtm) cc_final: 0.8136 (mtt) REVERT: C 245 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: D 301 PHE cc_start: 0.8415 (t80) cc_final: 0.8115 (t80) REVERT: D 397 MET cc_start: 0.8403 (ttm) cc_final: 0.8138 (ttt) REVERT: E 27 ASP cc_start: 0.7396 (p0) cc_final: 0.7064 (p0) REVERT: E 120 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8239 (mtt90) REVERT: E 144 MET cc_start: 0.8636 (mtt) cc_final: 0.8413 (mmt) REVERT: E 397 MET cc_start: 0.8289 (ttm) cc_final: 0.7859 (ttp) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 1.0302 time to fit residues: 115.1955 Evaluate side-chains 97 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064609 restraints weight = 94923.739| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.08 r_work: 0.2960 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14160 Z= 0.104 Angle : 0.444 6.434 19290 Z= 0.232 Chirality : 0.039 0.138 2165 Planarity : 0.004 0.092 2395 Dihedral : 3.722 20.368 2090 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.47 % Allowed : 7.32 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.21), residues: 1670 helix: 3.89 (0.21), residues: 550 sheet: -0.27 (0.25), residues: 430 loop : -0.06 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 190 TYR 0.007 0.001 TYR C 413 PHE 0.009 0.001 PHE A 301 TRP 0.020 0.001 TRP A 114 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00227 (14150) covalent geometry : angle 0.44270 (19265) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.80333 ( 10) hydrogen bonds : bond 0.03198 ( 710) hydrogen bonds : angle 3.97108 ( 2355) link_NAG-ASN : bond 0.00033 ( 5) link_NAG-ASN : angle 1.16918 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.84 seconds wall clock time: 83 minutes 15.91 seconds (4995.91 seconds total)