Starting phenix.real_space_refine on Fri Mar 6 22:10:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsu_54226/03_2026/9rsu_54226.map" } resolution = 2.1 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= 0.015 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 40 5.16 5 C 10952 2.51 5 N 2856 2.21 5 O 3416 1.98 5 H 16736 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34000 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4250 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 260} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 4.70, per 1000 atoms: 0.14 Number of scatterers: 34000 At special positions: 0 Unit cell: (114.924, 114.924, 111.996, 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 40 16.00 O 3416 8.00 N 2856 7.00 C 10952 6.00 H 16736 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 5.9% alpha, 78.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 213 through 218 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 213 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 34 removed outlier: 3.630A pdb=" N THR A 55 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 102 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS A 229 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE A 100 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 34 removed outlier: 3.630A pdb=" N THR A 55 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.911A pdb=" N ASN A 78 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 252 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR A 80 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR A 250 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP A 248 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 84 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 161 removed outlier: 6.500A pdb=" N SER A 167 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP A 161 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N SER A 83 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 78 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 252 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR A 80 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR A 250 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP A 248 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 84 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 128 removed outlier: 8.482A pdb=" N THR A 111 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU A 150 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR B 111 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU B 150 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR C 111 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU C 150 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR D 111 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU D 150 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR E 111 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU E 150 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR F 111 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU F 150 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR G 111 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU G 150 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR H 111 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU H 150 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR B 55 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B 102 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS B 229 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE B 100 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR B 55 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72 removed outlier: 5.911A pdb=" N ASN B 78 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 252 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR B 80 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR B 250 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP B 248 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 84 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 161 removed outlier: 6.500A pdb=" N SER B 167 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP B 161 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER B 83 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN B 78 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 252 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR B 80 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR B 250 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP B 248 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 84 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 34 removed outlier: 3.630A pdb=" N THR C 55 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 102 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS C 229 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE C 100 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 34 removed outlier: 3.630A pdb=" N THR C 55 " --> pdb=" O ILE C 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 72 removed outlier: 5.911A pdb=" N ASN C 78 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 252 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR C 80 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C 250 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP C 248 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 84 " --> pdb=" O TYR C 246 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 161 removed outlier: 6.500A pdb=" N SER C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP C 161 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER C 83 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 78 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 252 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR C 80 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C 250 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP C 248 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 84 " --> pdb=" O TYR C 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR D 55 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU D 102 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS D 229 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE D 100 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR D 55 " --> pdb=" O ILE D 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 69 through 72 removed outlier: 5.911A pdb=" N ASN D 78 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU D 252 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR D 80 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR D 250 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP D 248 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 84 " --> pdb=" O TYR D 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 154 through 161 removed outlier: 6.499A pdb=" N SER D 167 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP D 161 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS D 165 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER D 83 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN D 78 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU D 252 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR D 80 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR D 250 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP D 248 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 84 " --> pdb=" O TYR D 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR E 55 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU E 102 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS E 229 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE E 100 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR E 55 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 69 through 72 removed outlier: 5.910A pdb=" N ASN E 78 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 252 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR E 80 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR E 250 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP E 248 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 84 " --> pdb=" O TYR E 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 154 through 161 removed outlier: 6.499A pdb=" N SER E 167 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP E 161 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER E 83 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN E 78 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 252 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR E 80 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR E 250 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP E 248 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 84 " --> pdb=" O TYR E 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR F 55 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU F 102 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS F 229 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE F 100 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR F 55 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 69 through 72 removed outlier: 5.911A pdb=" N ASN F 78 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 252 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR F 80 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR F 250 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP F 248 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 84 " --> pdb=" O TYR F 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 154 through 161 removed outlier: 6.500A pdb=" N SER F 167 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP F 161 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS F 165 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER F 83 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN F 78 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 252 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR F 80 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR F 250 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP F 248 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 84 " --> pdb=" O TYR F 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR G 55 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU G 102 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS G 229 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE G 100 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR G 55 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN G 78 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU G 252 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR G 80 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR G 250 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP G 248 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 84 " --> pdb=" O TYR G 246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 154 through 161 removed outlier: 6.499A pdb=" N SER G 167 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP G 161 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS G 165 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER G 83 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN G 78 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU G 252 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR G 80 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR G 250 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP G 248 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 84 " --> pdb=" O TYR G 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR H 55 " --> pdb=" O ILE H 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU H 102 " --> pdb=" O ALA H 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS H 229 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE H 100 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 24 through 34 removed outlier: 3.629A pdb=" N THR H 55 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 69 through 72 removed outlier: 5.912A pdb=" N ASN H 78 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 252 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR H 80 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR H 250 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP H 248 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 84 " --> pdb=" O TYR H 246 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 154 through 161 removed outlier: 6.500A pdb=" N SER H 167 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP H 161 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS H 165 " --> pdb=" O ASP H 161 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER H 83 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN H 78 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 252 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR H 80 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR H 250 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP H 248 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 84 " --> pdb=" O TYR H 246 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3240 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: 9.09 Time building geometry restraints manager: 4.21 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: 16736 1.03 - 1.22: 0 1.22 - 1.42: 7669 1.42 - 1.61: 9915 1.61 - 1.80: 80 Bond restraints: 34400 Sorted by residual: bond pdb=" C ARG D 264 " pdb=" N VAL D 265 " ideal model delta sigma weight residual 1.334 1.324 0.010 1.29e-02 6.01e+03 6.33e-01 bond pdb=" C ARG B 264 " pdb=" N VAL B 265 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.29e-02 6.01e+03 5.42e-01 bond pdb=" C ARG H 264 " pdb=" N VAL H 265 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.29e-02 6.01e+03 5.42e-01 bond pdb=" C ARG F 264 " pdb=" N VAL F 265 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.29e-02 6.01e+03 5.42e-01 bond pdb=" C ARG E 264 " pdb=" N VAL E 265 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.29e-02 6.01e+03 5.33e-01 ... (remaining 34395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 56285 0.78 - 1.55: 5069 1.55 - 2.33: 462 2.33 - 3.11: 40 3.11 - 3.88: 48 Bond angle restraints: 61904 Sorted by residual: angle pdb=" CA ARG B 113 " pdb=" CB ARG B 113 " pdb=" CG ARG B 113 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA ARG D 113 " pdb=" CB ARG D 113 " pdb=" CG ARG D 113 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA ARG A 113 " pdb=" CB ARG A 113 " pdb=" CG ARG A 113 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA ARG F 113 " pdb=" CB ARG F 113 " pdb=" CG ARG F 113 " ideal model delta sigma weight residual 114.10 117.60 -3.50 2.00e+00 2.50e-01 3.06e+00 angle pdb=" CA ARG C 113 " pdb=" CB ARG C 113 " pdb=" CG ARG C 113 " ideal model delta sigma weight residual 114.10 117.59 -3.49 2.00e+00 2.50e-01 3.04e+00 ... (remaining 61899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 15424 17.06 - 34.13: 631 34.13 - 51.19: 193 51.19 - 68.25: 64 68.25 - 85.32: 24 Dihedral angle restraints: 16336 sinusoidal: 8736 harmonic: 7600 Sorted by residual: dihedral pdb=" CA TYR B 270 " pdb=" C TYR B 270 " pdb=" N TYR B 271 " pdb=" CA TYR B 271 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR D 270 " pdb=" C TYR D 270 " pdb=" N TYR D 271 " pdb=" CA TYR D 271 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR G 270 " pdb=" C TYR G 270 " pdb=" N TYR G 271 " pdb=" CA TYR G 271 " ideal model delta harmonic sigma weight residual 180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 16333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1495 0.027 - 0.055: 737 0.055 - 0.082: 135 0.082 - 0.109: 127 0.109 - 0.137: 82 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CA ILE E 87 " pdb=" N ILE E 87 " pdb=" C ILE E 87 " pdb=" CB ILE E 87 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE G 87 " pdb=" N ILE G 87 " pdb=" C ILE G 87 " pdb=" CB ILE G 87 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 87 " pdb=" N ILE A 87 " pdb=" C ILE A 87 " pdb=" CB ILE A 87 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.56e-01 ... (remaining 2573 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 255 " -0.012 2.00e-02 2.50e+03 6.01e-03 1.08e+00 pdb=" CG TYR D 255 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 255 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 255 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 255 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 255 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 255 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR D 255 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR D 255 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR D 255 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR D 255 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 255 " -0.011 2.00e-02 2.50e+03 5.91e-03 1.05e+00 pdb=" CG TYR C 255 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR C 255 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 255 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 255 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 255 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 255 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR C 255 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C 255 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR C 255 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR C 255 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 255 " -0.012 2.00e-02 2.50e+03 5.90e-03 1.05e+00 pdb=" CG TYR B 255 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 255 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 255 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 255 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 255 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 255 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR B 255 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 255 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR B 255 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 255 " 0.001 2.00e-02 2.50e+03 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.43: 17487 2.43 - 2.97: 75179 2.97 - 3.51: 83661 3.51 - 4.06: 123492 4.06 - 4.60: 173926 Nonbonded interactions: 473745 Sorted by model distance: nonbonded pdb="HE22 GLN A 144 " pdb="HD21 ASN B 142 " model vdw 1.883 2.100 nonbonded pdb="HE22 GLN G 144 " pdb="HD21 ASN H 142 " model vdw 1.883 2.100 nonbonded pdb=" HB3 GLN A 148 " pdb="HH12 ARG B 113 " model vdw 1.883 2.270 nonbonded pdb="HE22 GLN C 144 " pdb="HD21 ASN D 142 " model vdw 1.883 2.100 nonbonded pdb=" HB3 GLN G 148 " pdb="HH12 ARG H 113 " model vdw 1.883 2.270 ... (remaining 473740 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.560 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: 0.210 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.830 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17664 Z= 0.187 Angle : 0.456 3.882 23944 Z= 0.256 Chirality : 0.041 0.137 2576 Planarity : 0.003 0.025 3056 Dihedral : 11.145 85.319 6456 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.14 (0.17), residues: 2144 helix: -4.12 (0.23), residues: 48 sheet: 0.49 (0.15), residues: 1216 loop : -0.61 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 113 TYR 0.017 0.001 TYR C 255 PHE 0.004 0.001 PHE A 193 TRP 0.006 0.001 TRP A 168 HIS 0.001 0.000 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00441 (17664) covalent geometry : angle 0.45584 (23944) hydrogen bonds : bond 0.19432 ( 952) hydrogen bonds : angle 9.22954 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.854 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 258 GLN cc_start: 0.9035 (pm20) cc_final: 0.8797 (pm20) REVERT: D 258 GLN cc_start: 0.9034 (pm20) cc_final: 0.8798 (pm20) REVERT: F 258 GLN cc_start: 0.9034 (pm20) cc_final: 0.8797 (pm20) REVERT: H 258 GLN cc_start: 0.9035 (pm20) cc_final: 0.8799 (pm20) outliers start: 0 outliers final: 4 residues processed: 146 average time/residue: 2.5532 time to fit residues: 396.4371 Evaluate side-chains 139 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain H residue 224 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 182 ASN B 144 GLN B 182 ASN C 144 GLN C 182 ASN D 144 GLN D 182 ASN E 144 GLN E 182 ASN F 144 GLN F 182 ASN G 144 GLN G 182 ASN H 144 GLN H 182 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.060239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.048890 restraints weight = 93748.673| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.24 r_work: 0.2333 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17664 Z= 0.212 Angle : 0.521 4.679 23944 Z= 0.283 Chirality : 0.046 0.145 2576 Planarity : 0.004 0.026 3056 Dihedral : 5.008 51.970 2364 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.05 % Allowed : 2.41 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.57 (0.17), residues: 2144 helix: -3.74 (0.38), residues: 48 sheet: 0.99 (0.14), residues: 1328 loop : -0.36 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 113 TYR 0.013 0.001 TYR D 255 PHE 0.005 0.001 PHE B 220 TRP 0.009 0.001 TRP F 168 HIS 0.001 0.000 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00479 (17664) covalent geometry : angle 0.52113 (23944) hydrogen bonds : bond 0.03738 ( 952) hydrogen bonds : angle 5.42758 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.996 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 139 average time/residue: 2.5601 time to fit residues: 378.4939 Evaluate side-chains 136 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 224 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 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 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.059842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.048277 restraints weight = 94407.732| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.23 r_work: 0.2334 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2233 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 17664 Z= 0.206 Angle : 0.490 3.953 23944 Z= 0.269 Chirality : 0.044 0.144 2576 Planarity : 0.003 0.023 3056 Dihedral : 4.794 37.292 2364 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.42 % Allowed : 3.87 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.17), residues: 2144 helix: -3.38 (0.49), residues: 48 sheet: 1.13 (0.14), residues: 1328 loop : -0.27 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.009 0.001 TYR C 255 PHE 0.004 0.001 PHE G 45 TRP 0.006 0.001 TRP A 168 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd covalent geometry : bond 0.00467 (17664) covalent geometry : angle 0.49035 (23944) hydrogen bonds : bond 0.03721 ( 952) hydrogen bonds : angle 4.98857 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.941 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 2.4365 time to fit residues: 323.3278 Evaluate side-chains 120 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN C 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.060794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.049287 restraints weight = 93463.863| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 2.22 r_work: 0.2361 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17664 Z= 0.149 Angle : 0.457 3.820 23944 Z= 0.250 Chirality : 0.044 0.144 2576 Planarity : 0.003 0.024 3056 Dihedral : 4.361 16.345 2352 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.63 % Allowed : 3.87 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.17), residues: 2144 helix: -2.66 (0.59), residues: 48 sheet: 1.19 (0.13), residues: 1344 loop : -0.48 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.007 0.001 TYR D 255 PHE 0.005 0.001 PHE C 45 TRP 0.006 0.001 TRP A 168 HIS 0.001 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00333 (17664) covalent geometry : angle 0.45721 (23944) hydrogen bonds : bond 0.03201 ( 952) hydrogen bonds : angle 4.64284 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.954 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 140 average time/residue: 2.3748 time to fit residues: 354.4955 Evaluate side-chains 128 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 200 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.060516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.049041 restraints weight = 94168.800| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 2.23 r_work: 0.2353 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2252 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 17664 Z= 0.163 Angle : 0.465 3.830 23944 Z= 0.254 Chirality : 0.044 0.144 2576 Planarity : 0.003 0.026 3056 Dihedral : 4.373 16.401 2352 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.42 % Allowed : 4.34 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.17), residues: 2144 helix: -2.60 (0.60), residues: 48 sheet: 1.26 (0.13), residues: 1344 loop : -0.48 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 113 TYR 0.007 0.001 TYR C 255 PHE 0.005 0.001 PHE A 45 TRP 0.005 0.001 TRP B 168 HIS 0.002 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00369 (17664) covalent geometry : angle 0.46532 (23944) hydrogen bonds : bond 0.03232 ( 952) hydrogen bonds : angle 4.54365 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.975 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 2.5207 time to fit residues: 354.9625 Evaluate side-chains 128 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 3.9990 chunk 183 optimal weight: 0.1980 chunk 209 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN C 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.059942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.048425 restraints weight = 94545.202| |-----------------------------------------------------------------------------| r_work (start): 0.2449 rms_B_bonded: 2.23 r_work: 0.2338 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2236 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17664 Z= 0.191 Angle : 0.475 3.838 23944 Z= 0.259 Chirality : 0.044 0.145 2576 Planarity : 0.003 0.024 3056 Dihedral : 4.455 16.922 2352 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.63 % Allowed : 4.45 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.94 (0.17), residues: 2144 helix: -3.09 (0.57), residues: 48 sheet: 1.33 (0.13), residues: 1312 loop : -0.33 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 113 TYR 0.008 0.001 TYR D 255 PHE 0.006 0.001 PHE C 45 TRP 0.005 0.001 TRP A 168 HIS 0.002 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00435 (17664) covalent geometry : angle 0.47464 (23944) hydrogen bonds : bond 0.03361 ( 952) hydrogen bonds : angle 4.56417 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.007 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 132 average time/residue: 2.4680 time to fit residues: 347.9053 Evaluate side-chains 128 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.058241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.046913 restraints weight = 95624.028| |-----------------------------------------------------------------------------| r_work (start): 0.2398 rms_B_bonded: 2.23 r_work: 0.2288 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 17664 Z= 0.247 Angle : 0.496 3.880 23944 Z= 0.272 Chirality : 0.045 0.146 2576 Planarity : 0.003 0.025 3056 Dihedral : 4.577 17.338 2352 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.97 (0.17), residues: 2144 helix: -3.22 (0.53), residues: 48 sheet: 1.36 (0.13), residues: 1312 loop : -0.33 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.009 0.001 TYR D 255 PHE 0.006 0.001 PHE C 45 TRP 0.005 0.001 TRP F 168 HIS 0.002 0.001 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00568 (17664) covalent geometry : angle 0.49613 (23944) hydrogen bonds : bond 0.03577 ( 952) hydrogen bonds : angle 4.65035 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.976 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 2.4894 time to fit residues: 344.9986 Evaluate side-chains 126 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN C 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.059127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.047860 restraints weight = 95001.661| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 2.22 r_work: 0.2312 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17664 Z= 0.175 Angle : 0.470 4.726 23944 Z= 0.256 Chirality : 0.044 0.146 2576 Planarity : 0.003 0.027 3056 Dihedral : 4.472 17.651 2352 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.93 (0.17), residues: 2144 helix: -2.67 (0.58), residues: 48 sheet: 1.37 (0.13), residues: 1328 loop : -0.52 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 113 TYR 0.007 0.001 TYR C 255 PHE 0.006 0.001 PHE A 45 TRP 0.006 0.001 TRP B 168 HIS 0.001 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00394 (17664) covalent geometry : angle 0.47032 (23944) hydrogen bonds : bond 0.03296 ( 952) hydrogen bonds : angle 4.51246 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.884 Fit side-chains REVERT: C 113 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8607 (ttt90) REVERT: E 113 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8603 (ttt90) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 2.5649 time to fit residues: 359.9783 Evaluate side-chains 131 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 86 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.058087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.046901 restraints weight = 95585.867| |-----------------------------------------------------------------------------| r_work (start): 0.2399 rms_B_bonded: 2.20 r_work: 0.2288 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2187 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 17664 Z= 0.249 Angle : 0.502 4.742 23944 Z= 0.274 Chirality : 0.045 0.147 2576 Planarity : 0.003 0.027 3056 Dihedral : 4.597 17.918 2352 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.52 % Allowed : 4.60 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.99 (0.17), residues: 2144 helix: -3.21 (0.53), residues: 48 sheet: 1.37 (0.13), residues: 1312 loop : -0.32 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 113 TYR 0.008 0.001 TYR C 255 PHE 0.007 0.001 PHE G 45 TRP 0.005 0.001 TRP B 168 HIS 0.002 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00573 (17664) covalent geometry : angle 0.50250 (23944) hydrogen bonds : bond 0.03569 ( 952) hydrogen bonds : angle 4.64439 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.974 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 129 average time/residue: 2.4162 time to fit residues: 332.4270 Evaluate side-chains 131 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain H residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 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 144 GLN C 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.058504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.047215 restraints weight = 95776.630| |-----------------------------------------------------------------------------| r_work (start): 0.2407 rms_B_bonded: 2.23 r_work: 0.2298 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 17664 Z= 0.220 Angle : 0.493 4.582 23944 Z= 0.268 Chirality : 0.044 0.147 2576 Planarity : 0.003 0.028 3056 Dihedral : 4.580 18.457 2352 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.98 (0.17), residues: 2144 helix: -3.16 (0.55), residues: 48 sheet: 1.36 (0.13), residues: 1312 loop : -0.31 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.008 0.001 TYR D 255 PHE 0.006 0.001 PHE G 45 TRP 0.006 0.001 TRP D 168 HIS 0.002 0.001 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00502 (17664) covalent geometry : angle 0.49262 (23944) hydrogen bonds : bond 0.03465 ( 952) hydrogen bonds : angle 4.59452 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 1.082 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 2.4900 time to fit residues: 358.0738 Evaluate side-chains 134 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 144 GLN D 144 GLN E 144 GLN F 144 GLN G 144 GLN H 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.058022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.046848 restraints weight = 95618.332| |-----------------------------------------------------------------------------| r_work (start): 0.2398 rms_B_bonded: 2.20 r_work: 0.2288 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 17664 Z= 0.249 Angle : 0.509 4.807 23944 Z= 0.277 Chirality : 0.045 0.147 2576 Planarity : 0.003 0.028 3056 Dihedral : 4.628 18.819 2352 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.17), residues: 2144 helix: -3.23 (0.53), residues: 48 sheet: 1.41 (0.13), residues: 1304 loop : -0.34 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 113 TYR 0.008 0.001 TYR D 255 PHE 0.007 0.001 PHE G 45 TRP 0.005 0.001 TRP H 168 HIS 0.002 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00572 (17664) covalent geometry : angle 0.50856 (23944) hydrogen bonds : bond 0.03583 ( 952) hydrogen bonds : angle 4.65293 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12500.93 seconds wall clock time: 211 minutes 47.11 seconds (12707.11 seconds total)