Starting phenix.real_space_refine on Mon Aug 25 11:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhm_16060/08_2025/8bhm_16060.map" } resolution = 2.95 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= 0.068 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 8920 2.51 5 N 2270 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 27180 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 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 Restraints were copied for chains: B, C, D, E Time building chain proxies: 5.12, per 1000 atoms: 0.19 Number of scatterers: 27180 At special positions: 0 Unit cell: (94.01, 92.904, 123.872, 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 2270 7.00 C 8920 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: 2.39 Conformation dependent library (CDL) restraints added in 669.6 milliseconds Enol-peptide restraints added in 953.7 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: 50 helices and 20 sheets defined 41.4% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.624A 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: 3.531A 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: 3.789A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.001A 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: 3.624A 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: 3.531A 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: 3.788A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.001A 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: 3.624A 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: 3.531A 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: 3.789A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.001A 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: 3.624A 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: 3.531A 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: 3.788A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.001A 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: 3.624A 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: 3.530A 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: 3.789A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.002A 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: 6.594A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.387A 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: 7.130A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.387A 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: 4.761A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.594A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 124 removed outlier: 7.130A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 112 removed outlier: 6.594A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 124 removed outlier: 7.131A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 112 removed outlier: 6.594A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 124 removed outlier: 7.131A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.760A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.760A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.594A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 120 through 124 removed outlier: 7.130A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2415 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: 5.29 Time building geometry restraints manager: 3.29 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: 5 1.23 - 1.42: 6120 1.42 - 1.61: 7860 1.61 - 1.81: 150 Bond restraints: 27550 Sorted by residual: bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.53e+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 2.51e+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 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+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 27545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 47796 1.10 - 2.21: 1592 2.21 - 3.31: 82 3.31 - 4.42: 35 4.42 - 5.52: 10 Bond angle restraints: 49515 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 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.40e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.19 -5.49 1.80e+00 3.09e-01 9.32e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.18 -5.48 1.80e+00 3.09e-01 9.25e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.16 -5.46 1.80e+00 3.09e-01 9.21e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.16 -5.46 1.80e+00 3.09e-01 9.21e+00 ... (remaining 49510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 12735 17.60 - 35.21: 220 35.21 - 52.81: 135 52.81 - 70.41: 45 70.41 - 88.02: 25 Dihedral angle restraints: 13160 sinusoidal: 7030 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " pdb=" CD LYS A 315 " pdb=" CE LYS A 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.99 -40.99 3 1.50e+01 4.44e-03 7.32e+00 dihedral pdb=" CB LYS E 315 " pdb=" CG LYS E 315 " pdb=" CD LYS E 315 " pdb=" CE LYS E 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.96 -40.96 3 1.50e+01 4.44e-03 7.31e+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 60.00 100.92 -40.92 3 1.50e+01 4.44e-03 7.31e+00 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1271 0.024 - 0.048: 572 0.048 - 0.072: 161 0.072 - 0.096: 66 0.096 - 0.121: 90 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 2157 not shown) Planarity restraints: 3990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 R63 C 502 " -0.002 2.00e-02 2.50e+03 1.10e-02 5.18e+00 pdb=" C03 R63 C 502 " 0.003 2.00e-02 2.50e+03 pdb=" C04 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C05 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C06 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C07 R63 C 502 " 0.004 2.00e-02 2.50e+03 pdb=" C08 R63 C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C09 R63 C 502 " -0.001 2.00e-02 2.50e+03 pdb=" C10 R63 C 502 " 0.006 2.00e-02 2.50e+03 pdb=" C12 R63 C 502 " 0.008 2.00e-02 2.50e+03 pdb=" C13 R63 C 502 " 0.001 2.00e-02 2.50e+03 pdb=" C15 R63 C 502 " -0.005 2.00e-02 2.50e+03 pdb=" C16 R63 C 502 " -0.019 2.00e-02 2.50e+03 pdb=" N11 R63 C 502 " 0.007 2.00e-02 2.50e+03 pdb=" N14 R63 C 502 " -0.005 2.00e-02 2.50e+03 pdb=" O20 R63 C 502 " -0.032 2.00e-02 2.50e+03 pdb=" O22 R63 C 502 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R63 A 502 " 0.002 2.00e-02 2.50e+03 1.10e-02 5.12e+00 pdb=" C03 R63 A 502 " -0.004 2.00e-02 2.50e+03 pdb=" C04 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C05 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C06 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C07 R63 A 502 " -0.003 2.00e-02 2.50e+03 pdb=" C08 R63 A 502 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R63 A 502 " 0.002 2.00e-02 2.50e+03 pdb=" C10 R63 A 502 " -0.007 2.00e-02 2.50e+03 pdb=" C12 R63 A 502 " -0.008 2.00e-02 2.50e+03 pdb=" C13 R63 A 502 " -0.001 2.00e-02 2.50e+03 pdb=" C15 R63 A 502 " 0.005 2.00e-02 2.50e+03 pdb=" C16 R63 A 502 " 0.019 2.00e-02 2.50e+03 pdb=" N11 R63 A 502 " -0.007 2.00e-02 2.50e+03 pdb=" N14 R63 A 502 " 0.005 2.00e-02 2.50e+03 pdb=" O20 R63 A 502 " 0.032 2.00e-02 2.50e+03 pdb=" O22 R63 A 502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R63 E 502 " 0.002 2.00e-02 2.50e+03 1.10e-02 5.11e+00 pdb=" C03 R63 E 502 " -0.003 2.00e-02 2.50e+03 pdb=" C04 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C05 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C06 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C07 R63 E 502 " -0.004 2.00e-02 2.50e+03 pdb=" C08 R63 E 502 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R63 E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C10 R63 E 502 " -0.006 2.00e-02 2.50e+03 pdb=" C12 R63 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" C13 R63 E 502 " -0.002 2.00e-02 2.50e+03 pdb=" C15 R63 E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C16 R63 E 502 " 0.019 2.00e-02 2.50e+03 pdb=" N11 R63 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" N14 R63 E 502 " 0.005 2.00e-02 2.50e+03 pdb=" O20 R63 E 502 " 0.032 2.00e-02 2.50e+03 pdb=" O22 R63 E 502 " -0.010 2.00e-02 2.50e+03 ... (remaining 3987 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 2945 2.26 - 2.85: 62121 2.85 - 3.43: 68314 3.43 - 4.02: 97986 4.02 - 4.60: 149501 Nonbonded interactions: 380867 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.677 2.450 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.677 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.677 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.678 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.678 2.450 ... (remaining 380862 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: 0.06 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: 1.630 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: 0.090 Extract box with map and model: 0.230 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.980 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 0.029 14145 Z= 0.085 Angle : 0.372 5.520 19265 Z= 0.174 Chirality : 0.037 0.121 2160 Planarity : 0.003 0.024 2385 Dihedral : 8.674 88.018 5150 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 1.79 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 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: 2.44 (0.22), residues: 1670 helix: 3.28 (0.22), residues: 585 sheet: 0.80 (0.27), residues: 435 loop : 0.74 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.004 0.001 TYR D 285 PHE 0.003 0.000 PHE C 149 TRP 0.002 0.000 TRP D 73 HIS 0.002 0.000 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00179 (14135) covalent geometry : angle 0.36933 (19240) SS BOND : bond 0.00050 ( 5) SS BOND : angle 0.27207 ( 10) hydrogen bonds : bond 0.24356 ( 715) hydrogen bonds : angle 7.58935 ( 2415) link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 1.59424 ( 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 145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.561 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 CYS cc_start: 0.9496 (m) cc_final: 0.9210 (m) REVERT: A 289 MET cc_start: 0.9160 (ttp) cc_final: 0.8935 (ttm) REVERT: B 197 MET cc_start: 0.9212 (mmm) cc_final: 0.9003 (mmp) REVERT: B 237 CYS cc_start: 0.9465 (m) cc_final: 0.9204 (m) REVERT: C 197 MET cc_start: 0.9220 (mmm) cc_final: 0.8962 (mmm) REVERT: C 289 MET cc_start: 0.9151 (ttp) cc_final: 0.8919 (ttm) REVERT: D 289 MET cc_start: 0.9123 (ttp) cc_final: 0.8911 (ttm) REVERT: E 289 MET cc_start: 0.9149 (ttp) cc_final: 0.8933 (ttm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.2236 time to fit residues: 193.4897 Evaluate side-chains 111 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.2936 r_free = 0.2936 target = 0.055480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.046816 restraints weight = 126438.872| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.46 r_work: 0.2548 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14145 Z= 0.209 Angle : 0.537 6.119 19265 Z= 0.285 Chirality : 0.040 0.152 2160 Planarity : 0.006 0.091 2385 Dihedral : 9.620 89.505 2015 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 4.50 % Favored : 94.50 % 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: 2.21 (0.21), residues: 1670 helix: 3.18 (0.20), residues: 610 sheet: 0.74 (0.28), residues: 410 loop : 0.32 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 190 TYR 0.009 0.001 TYR A 413 PHE 0.009 0.001 PHE A 68 TRP 0.011 0.001 TRP D 174 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00457 (14135) covalent geometry : angle 0.53616 (19240) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.31888 ( 10) hydrogen bonds : bond 0.05209 ( 715) hydrogen bonds : angle 5.20132 ( 2415) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 1.50014 ( 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 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.690 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: symmetry clash REVERT: B 27 ASP cc_start: 0.9168 (t0) cc_final: 0.8901 (p0) REVERT: B 232 GLN cc_start: 0.9332 (tp40) cc_final: 0.9108 (tp40) REVERT: C 27 ASP cc_start: 0.9152 (t0) cc_final: 0.8914 (p0) REVERT: C 232 GLN cc_start: 0.9341 (tp40) cc_final: 0.9067 (tp40) REVERT: C 289 MET cc_start: 0.9101 (ttp) cc_final: 0.8896 (ttm) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 1.1076 time to fit residues: 153.7832 Evaluate side-chains 116 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.2870 r_free = 0.2870 target = 0.053065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.044363 restraints weight = 129737.319| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.37 r_work: 0.2487 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14145 Z= 0.243 Angle : 0.527 6.922 19265 Z= 0.277 Chirality : 0.040 0.139 2160 Planarity : 0.005 0.062 2385 Dihedral : 9.469 88.846 2015 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.14 % Allowed : 5.10 % Favored : 93.76 % 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: 1.97 (0.21), residues: 1670 helix: 3.19 (0.21), residues: 610 sheet: 0.32 (0.27), residues: 410 loop : 0.19 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 190 TYR 0.010 0.001 TYR C 297 PHE 0.010 0.001 PHE E 69 TRP 0.006 0.001 TRP C 249 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00525 (14135) covalent geometry : angle 0.52541 (19240) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.34383 ( 10) hydrogen bonds : bond 0.04586 ( 715) hydrogen bonds : angle 4.71182 ( 2415) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 1.70181 ( 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 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.543 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: C 232 GLN cc_start: 0.9412 (tp40) cc_final: 0.9144 (tp40) REVERT: C 289 MET cc_start: 0.9258 (ttp) cc_final: 0.9051 (ttm) REVERT: D 216 MET cc_start: 0.9115 (mmm) cc_final: 0.8765 (mmm) REVERT: E 62 GLU cc_start: 0.8333 (pp20) cc_final: 0.8113 (pp20) REVERT: E 289 MET cc_start: 0.9399 (ttm) cc_final: 0.8683 (ttm) outliers start: 17 outliers final: 11 residues processed: 114 average time/residue: 1.2769 time to fit residues: 161.8095 Evaluate side-chains 106 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU 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 142 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.053606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.044925 restraints weight = 128338.638| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.35 r_work: 0.2498 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14145 Z= 0.179 Angle : 0.495 7.736 19265 Z= 0.254 Chirality : 0.039 0.137 2160 Planarity : 0.004 0.041 2385 Dihedral : 9.270 89.587 2015 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.81 % Allowed : 6.17 % Favored : 93.02 % 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: 1.95 (0.21), residues: 1670 helix: 3.32 (0.21), residues: 610 sheet: 0.21 (0.28), residues: 385 loop : 0.08 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.009 0.001 TYR E 297 PHE 0.009 0.001 PHE A 307 TRP 0.005 0.001 TRP D 73 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00386 (14135) covalent geometry : angle 0.49307 (19240) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.48160 ( 10) hydrogen bonds : bond 0.03968 ( 715) hydrogen bonds : angle 4.43072 ( 2415) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 1.69519 ( 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 112 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.775 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: C 216 MET cc_start: 0.9174 (mmm) cc_final: 0.8792 (mmm) REVERT: C 232 GLN cc_start: 0.9420 (tp40) cc_final: 0.9138 (tp40) REVERT: C 289 MET cc_start: 0.9281 (ttp) cc_final: 0.9078 (ttm) REVERT: D 216 MET cc_start: 0.9076 (mmm) cc_final: 0.8822 (mmm) REVERT: D 289 MET cc_start: 0.9207 (ttp) cc_final: 0.8907 (ttm) REVERT: E 62 GLU cc_start: 0.8289 (pp20) cc_final: 0.8085 (pp20) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 1.3506 time to fit residues: 158.3924 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 : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 148 optimal weight: 0.0020 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.045143 restraints weight = 128417.651| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 3.43 r_work: 0.2483 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14145 Z= 0.199 Angle : 0.501 8.900 19265 Z= 0.256 Chirality : 0.039 0.133 2160 Planarity : 0.004 0.042 2385 Dihedral : 8.650 87.106 2015 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 1.94 (0.21), residues: 1670 helix: 3.41 (0.21), residues: 610 sheet: 0.03 (0.26), residues: 410 loop : 0.11 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR E 297 PHE 0.009 0.001 PHE A 307 TRP 0.006 0.001 TRP A 114 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00430 (14135) covalent geometry : angle 0.49891 (19240) SS BOND : bond 0.00311 ( 5) SS BOND : angle 0.52681 ( 10) hydrogen bonds : bond 0.03835 ( 715) hydrogen bonds : angle 4.33153 ( 2415) link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.76168 ( 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 116 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.838 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: C 216 MET cc_start: 0.9139 (mmm) cc_final: 0.8812 (mmm) REVERT: C 232 GLN cc_start: 0.9431 (tp40) cc_final: 0.9225 (tp40) REVERT: C 289 MET cc_start: 0.9289 (ttp) cc_final: 0.9077 (ttm) REVERT: D 289 MET cc_start: 0.9244 (ttp) cc_final: 0.8963 (ttm) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 1.3220 time to fit residues: 161.2708 Evaluate side-chains 107 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.045318 restraints weight = 128172.775| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.43 r_work: 0.2488 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14145 Z= 0.179 Angle : 0.499 9.045 19265 Z= 0.253 Chirality : 0.039 0.133 2160 Planarity : 0.004 0.043 2385 Dihedral : 7.897 88.116 2015 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.74 % Allowed : 6.98 % 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: 1.96 (0.21), residues: 1670 helix: 3.49 (0.21), residues: 610 sheet: -0.03 (0.26), residues: 410 loop : 0.10 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR E 297 PHE 0.008 0.001 PHE A 307 TRP 0.006 0.001 TRP A 114 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00388 (14135) covalent geometry : angle 0.49638 (19240) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.58161 ( 10) hydrogen bonds : bond 0.03687 ( 715) hydrogen bonds : angle 4.24799 ( 2415) link_NAG-ASN : bond 0.00106 ( 5) link_NAG-ASN : angle 1.75839 ( 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: 11 poor density : 101 time to evaluate : 0.820 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: C 216 MET cc_start: 0.9123 (mmm) cc_final: 0.8731 (mmm) REVERT: C 232 GLN cc_start: 0.9436 (tp40) cc_final: 0.9232 (tp40) REVERT: C 289 MET cc_start: 0.9315 (ttp) cc_final: 0.9090 (ttm) REVERT: D 289 MET cc_start: 0.9265 (ttp) cc_final: 0.9003 (ttm) REVERT: E 280 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8228 (tm) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 1.3270 time to fit residues: 157.9394 Evaluate side-chains 110 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.044460 restraints weight = 129135.505| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.35 r_work: 0.2489 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14145 Z= 0.194 Angle : 0.508 9.654 19265 Z= 0.257 Chirality : 0.039 0.156 2160 Planarity : 0.004 0.044 2385 Dihedral : 6.948 89.901 2015 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.81 % Allowed : 7.45 % Favored : 91.74 % 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: 1.93 (0.21), residues: 1670 helix: 3.51 (0.21), residues: 610 sheet: -0.08 (0.26), residues: 410 loop : 0.06 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR B 413 PHE 0.008 0.001 PHE A 307 TRP 0.005 0.001 TRP D 174 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00420 (14135) covalent geometry : angle 0.50553 (19240) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.59973 ( 10) hydrogen bonds : bond 0.03644 ( 715) hydrogen bonds : angle 4.22742 ( 2415) link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.77220 ( 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: 12 poor density : 98 time to evaluate : 0.745 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: C 216 MET cc_start: 0.9128 (mmm) cc_final: 0.8773 (mmm) REVERT: C 232 GLN cc_start: 0.9436 (tp40) cc_final: 0.9236 (tp40) REVERT: C 289 MET cc_start: 0.9328 (ttp) cc_final: 0.9106 (ttm) REVERT: E 280 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8214 (tm) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 1.3090 time to fit residues: 150.6588 Evaluate side-chains 109 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.052319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.043763 restraints weight = 130935.793| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.31 r_work: 0.2468 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14145 Z= 0.255 Angle : 0.541 9.966 19265 Z= 0.276 Chirality : 0.040 0.171 2160 Planarity : 0.004 0.046 2385 Dihedral : 6.107 76.780 2015 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.07 % Allowed : 7.18 % Favored : 91.74 % 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: 1.83 (0.21), residues: 1670 helix: 3.42 (0.21), residues: 610 sheet: -0.19 (0.26), residues: 410 loop : 0.05 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.010 0.001 TYR E 297 PHE 0.010 0.001 PHE A 307 TRP 0.007 0.001 TRP A 114 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00551 (14135) covalent geometry : angle 0.53910 (19240) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.66237 ( 10) hydrogen bonds : bond 0.03801 ( 715) hydrogen bonds : angle 4.33717 ( 2415) link_NAG-ASN : bond 0.00211 ( 5) link_NAG-ASN : angle 1.83466 ( 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 113 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.845 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: B 197 MET cc_start: 0.9301 (mmp) cc_final: 0.9098 (mmp) REVERT: C 216 MET cc_start: 0.9139 (mmm) cc_final: 0.8775 (mmm) REVERT: C 289 MET cc_start: 0.9352 (ttp) cc_final: 0.9111 (ttm) REVERT: D 289 MET cc_start: 0.9287 (ttp) cc_final: 0.8955 (ttm) outliers start: 16 outliers final: 7 residues processed: 104 average time/residue: 1.3143 time to fit residues: 151.7249 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.045267 restraints weight = 128577.186| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.53 r_work: 0.2501 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14145 Z= 0.122 Angle : 0.507 10.928 19265 Z= 0.250 Chirality : 0.039 0.149 2160 Planarity : 0.004 0.044 2385 Dihedral : 5.349 63.858 2015 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.67 % Allowed : 7.72 % Favored : 91.61 % 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: 2.05 (0.21), residues: 1670 helix: 3.64 (0.21), residues: 610 sheet: -0.01 (0.27), residues: 385 loop : 0.08 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.008 0.001 TYR E 297 PHE 0.008 0.001 PHE A 301 TRP 0.007 0.001 TRP E 114 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00269 (14135) covalent geometry : angle 0.50507 (19240) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.63262 ( 10) hydrogen bonds : bond 0.03401 ( 715) hydrogen bonds : angle 4.05313 ( 2415) link_NAG-ASN : bond 0.00029 ( 5) link_NAG-ASN : angle 1.73863 ( 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 112 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8916 (mtm) cc_final: 0.8662 (mtm) REVERT: C 216 MET cc_start: 0.9082 (mmm) cc_final: 0.8746 (mmm) REVERT: C 289 MET cc_start: 0.9334 (ttp) cc_final: 0.9094 (ttm) REVERT: E 60 GLU cc_start: 0.8967 (mp0) cc_final: 0.8765 (mp0) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 1.2917 time to fit residues: 150.6633 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 : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 87 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.055540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.046501 restraints weight = 127879.813| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.47 r_work: 0.2543 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14145 Z= 0.097 Angle : 0.514 10.231 19265 Z= 0.250 Chirality : 0.039 0.144 2160 Planarity : 0.004 0.043 2385 Dihedral : 4.711 41.236 2015 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.34 % Allowed : 8.39 % Favored : 91.28 % 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: 2.21 (0.21), residues: 1670 helix: 3.79 (0.20), residues: 610 sheet: 0.10 (0.27), residues: 385 loop : 0.13 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR D 297 PHE 0.008 0.001 PHE D 261 TRP 0.009 0.001 TRP C 114 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00222 (14135) covalent geometry : angle 0.51250 (19240) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.62110 ( 10) hydrogen bonds : bond 0.03133 ( 715) hydrogen bonds : angle 3.86041 ( 2415) link_NAG-ASN : bond 0.00056 ( 5) link_NAG-ASN : angle 1.66896 ( 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 110 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8764 (mtm) cc_final: 0.8516 (mtm) REVERT: C 216 MET cc_start: 0.8999 (mmm) cc_final: 0.8710 (mmm) REVERT: C 289 MET cc_start: 0.9309 (ttp) cc_final: 0.9066 (ttm) REVERT: E 60 GLU cc_start: 0.8953 (mp0) cc_final: 0.8735 (mp0) REVERT: E 302 SER cc_start: 0.9460 (m) cc_final: 0.9249 (p) outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 1.3066 time to fit residues: 156.8803 Evaluate side-chains 105 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.054801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.045822 restraints weight = 127790.442| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.44 r_work: 0.2525 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14145 Z= 0.131 Angle : 0.527 11.811 19265 Z= 0.257 Chirality : 0.039 0.145 2160 Planarity : 0.004 0.044 2385 Dihedral : 4.558 41.932 2015 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.40 % Allowed : 8.59 % Favored : 91.01 % 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: 2.19 (0.21), residues: 1670 helix: 3.80 (0.20), residues: 610 sheet: 0.05 (0.27), residues: 385 loop : 0.11 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR E 297 PHE 0.008 0.001 PHE A 68 TRP 0.008 0.001 TRP E 114 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00291 (14135) covalent geometry : angle 0.52544 (19240) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.62519 ( 10) hydrogen bonds : bond 0.03203 ( 715) hydrogen bonds : angle 3.90109 ( 2415) link_NAG-ASN : bond 0.00027 ( 5) link_NAG-ASN : angle 1.65052 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5599.83 seconds wall clock time: 96 minutes 22.47 seconds (5782.47 seconds total)