Starting phenix.real_space_refine on Fri Sep 11 17:22:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lht_0897/09_2026/6lht_0897.cif" } resolution = 3.67 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= -0.025 sd= 1.249 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6916 2.51 5 N 1800 2.21 5 O 1969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10754 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 888 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 943 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 19, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 19, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.23 Number of scatterers: 10754 At special positions: 0 Unit cell: (143.77, 142.463, 99.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1969 8.00 N 1800 7.00 C 6916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 318.6 milliseconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 18 sheets defined 12.0% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.541A pdb=" N PHE A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.649A pdb=" N LYS A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.945A pdb=" N TRP A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 172 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.565A pdb=" N ASN A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 219 " --> pdb=" O GLN A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 219' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.661A pdb=" N ASN A 228 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 229' Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.540A pdb=" N PHE C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 3.649A pdb=" N LYS C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.945A pdb=" N TRP C 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 172 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 173 " --> pdb=" O ALA C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 173' Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.566A pdb=" N ASN C 218 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.662A pdb=" N ASN C 228 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 229 " --> pdb=" O PRO C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.541A pdb=" N PHE D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.649A pdb=" N LYS D 122 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.944A pdb=" N TRP D 171 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 172 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR D 173 " --> pdb=" O ALA D 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 173' Processing helix chain 'D' and resid 215 through 219 removed outlier: 3.566A pdb=" N ASN D 218 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 219 " --> pdb=" O GLN D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 219' Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.660A pdb=" N ASN D 228 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET D 229 " --> pdb=" O PRO D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'E' and resid 79 through 85 removed outlier: 3.542A pdb=" N PHE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.649A pdb=" N LYS E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 removed outlier: 3.945A pdb=" N TRP E 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 172 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR E 173 " --> pdb=" O ALA E 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 173' Processing helix chain 'E' and resid 215 through 219 removed outlier: 3.565A pdb=" N ASN E 218 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 219 " --> pdb=" O GLN E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 219' Processing helix chain 'E' and resid 225 through 229 removed outlier: 3.660A pdb=" N ASN E 228 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET E 229 " --> pdb=" O PRO E 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 225 through 229' Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.542A pdb=" N PHE B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.648A pdb=" N LYS B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.945A pdb=" N TRP B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 172 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 173 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 173' Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.566A pdb=" N ASN B 218 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 219 " --> pdb=" O GLN B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 219' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.660A pdb=" N ASN B 228 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing sheet with id=AA1, first strand: chain 'H' and resid 36 through 40 removed outlier: 3.733A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 92 through 94 removed outlier: 3.678A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 97 through 98 removed outlier: 4.126A pdb=" N ILE H 98 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR H 109 " --> pdb=" O ILE H 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU A 89 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET A 253 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 91 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 188 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU A 89 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET A 253 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 91 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 110 removed outlier: 3.654A pdb=" N VAL A 181 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU C 89 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET C 253 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 91 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 258 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 130 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 260 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR C 128 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE C 262 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE C 126 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 188 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU C 89 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET C 253 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 91 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 258 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 130 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 260 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR C 128 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE C 262 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE C 126 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL C 181 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU D 89 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 253 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D 91 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL D 258 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 130 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA D 260 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR D 128 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE D 262 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE D 126 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 188 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU D 89 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 253 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D 91 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL D 258 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 130 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA D 260 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR D 128 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE D 262 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE D 126 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 106 through 110 removed outlier: 3.654A pdb=" N VAL D 181 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU E 89 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET E 253 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 91 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL E 258 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG E 130 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA E 260 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR E 128 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE E 262 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE E 126 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 188 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU E 89 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET E 253 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 91 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL E 258 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG E 130 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA E 260 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR E 128 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE E 262 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE E 126 " --> pdb=" O ILE E 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL E 181 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU B 89 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 253 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 91 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 258 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG B 130 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA B 260 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR B 128 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 262 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 126 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 188 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 88 through 95 removed outlier: 6.082A pdb=" N LEU B 89 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 253 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 91 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 258 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG B 130 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA B 260 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR B 128 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 262 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 126 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL B 181 " --> pdb=" O LEU B 151 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 765 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: 1.06 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1697 1.31 - 1.45: 3295 1.45 - 1.59: 5961 1.59 - 1.72: 0 1.72 - 1.86: 119 Bond restraints: 11072 Sorted by residual: bond pdb=" N SER L 58 " pdb=" CA SER L 58 " ideal model delta sigma weight residual 1.457 1.356 0.101 1.29e-02 6.01e+03 6.16e+01 bond pdb=" C ASN H 52 " pdb=" N PRO H 53 " ideal model delta sigma weight residual 1.333 1.376 -0.043 7.80e-03 1.64e+04 3.04e+01 bond pdb=" C PRO A 148 " pdb=" O PRO A 148 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.13e-02 7.83e+03 2.71e+01 bond pdb=" N GLU L 61 " pdb=" CA GLU L 61 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.24e-02 6.50e+03 2.55e+01 bond pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.33e-02 5.65e+03 2.28e+01 ... (remaining 11067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 14944 5.34 - 10.68: 82 10.68 - 16.02: 13 16.02 - 21.36: 1 21.36 - 26.70: 1 Bond angle restraints: 15041 Sorted by residual: angle pdb=" N THR L 59 " pdb=" CA THR L 59 " pdb=" C THR L 59 " ideal model delta sigma weight residual 107.67 80.97 26.70 2.09e+00 2.29e-01 1.63e+02 angle pdb=" N ILE L 54 " pdb=" CA ILE L 54 " pdb=" C ILE L 54 " ideal model delta sigma weight residual 110.72 121.14 -10.42 1.01e+00 9.80e-01 1.07e+02 angle pdb=" C VAL L 64 " pdb=" N PRO L 65 " pdb=" CA PRO L 65 " ideal model delta sigma weight residual 119.84 107.91 11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" N THR H 69 " pdb=" CA THR H 69 " pdb=" C THR H 69 " ideal model delta sigma weight residual 110.42 96.54 13.88 1.46e+00 4.69e-01 9.04e+01 angle pdb=" N ASN H 61 " pdb=" CA ASN H 61 " pdb=" C ASN H 61 " ideal model delta sigma weight residual 112.86 102.76 10.10 1.22e+00 6.72e-01 6.85e+01 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5830 17.98 - 35.95: 595 35.95 - 53.93: 128 53.93 - 71.91: 25 71.91 - 89.88: 13 Dihedral angle restraints: 6591 sinusoidal: 2694 harmonic: 3897 Sorted by residual: dihedral pdb=" CA ASP H 50 " pdb=" C ASP H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual -180.00 -119.18 -60.82 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA TYR L 98 " pdb=" C TYR L 98 " pdb=" N ASN L 99 " pdb=" CA ASN L 99 " ideal model delta harmonic sigma weight residual -180.00 -124.96 -55.04 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LEU L 79 " pdb=" C LEU L 79 " pdb=" N THR L 80 " pdb=" CA THR L 80 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1502 0.132 - 0.263: 61 0.263 - 0.395: 16 0.395 - 0.527: 2 0.527 - 0.658: 1 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CA PHE H 64 " pdb=" N PHE H 64 " pdb=" C PHE H 64 " pdb=" CB PHE H 64 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PHE H 59 " pdb=" N PHE H 59 " pdb=" C PHE H 59 " pdb=" CB PHE H 59 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA GLN H 62 " pdb=" N GLN H 62 " pdb=" C GLN H 62 " pdb=" CB GLN H 62 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 1579 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 57 " -0.022 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ALA L 57 " 0.088 2.00e-02 2.50e+03 pdb=" O ALA L 57 " -0.036 2.00e-02 2.50e+03 pdb=" N SER L 58 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 98 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C TYR L 98 " 0.059 2.00e-02 2.50e+03 pdb=" O TYR L 98 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN L 99 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 52 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C LEU L 52 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU L 52 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU L 53 " 0.018 2.00e-02 2.50e+03 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 29 2.43 - 3.05: 6051 3.05 - 3.66: 15049 3.66 - 4.28: 21712 4.28 - 4.90: 36661 Nonbonded interactions: 79502 Sorted by model distance: nonbonded pdb=" O LYS H 67 " pdb=" O GLN H 82 " model vdw 1.810 3.040 nonbonded pdb=" CG PRO L 50 " pdb=" OG1 THR L 59 " model vdw 2.077 3.440 nonbonded pdb=" O ALA H 68 " pdb=" C THR H 69 " model vdw 2.175 3.270 nonbonded pdb=" O ALA L 57 " pdb=" O SER L 58 " model vdw 2.240 3.040 nonbonded pdb=" O SER L 32 " pdb=" OH TYR L 97 " model vdw 2.247 3.040 ... (remaining 79497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 71 through 295 or resid 301)) selection = chain 'C' selection = (chain 'D' and (resid 71 through 295 or resid 301)) selection = (chain 'E' and (resid 71 through 295 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.007 0.101 11074 Z= 0.406 Angle : 1.131 26.699 15045 Z= 0.645 Chirality : 0.072 0.658 1582 Planarity : 0.009 0.079 1927 Dihedral : 15.340 89.881 4083 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.74 % Favored : 92.72 % Rotamer: Outliers : 2.05 % Allowed : 9.12 % Favored : 88.83 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.25 % 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: -4.42 (0.19), residues: 1305 helix: -4.97 (0.10), residues: 100 sheet: -1.75 (0.27), residues: 326 loop : -3.40 (0.16), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 254 TYR 0.040 0.002 TYR L 55 PHE 0.032 0.002 PHE H 107 TRP 0.019 0.002 TRP L 102 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.41 (11072) covalent geometry : angle 1.12976 / 0.64 (15041) SS BOND : bond 0.01375 / 0.72 ( 2) SS BOND : angle 2.82795 / 1.60 ( 4) hydrogen bonds : bond 0.27681 / 18.05 ( 202) hydrogen bonds : angle 10.58894 / 7.17 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 369 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 39 LEU cc_start: 0.7238 (tp) cc_final: 0.6551 (tp) REVERT: L 44 GLN cc_start: 0.6787 (mp10) cc_final: 0.6564 (mp10) REVERT: L 98 TYR cc_start: 0.6329 (t80) cc_final: 0.5983 (t80) REVERT: H 33 TYR cc_start: 0.7319 (m-10) cc_final: 0.7109 (m-10) REVERT: H 57 ASP cc_start: 0.8592 (p0) cc_final: 0.8204 (p0) REVERT: A 173 THR cc_start: 0.9302 (p) cc_final: 0.9012 (p) REVERT: A 229 MET cc_start: 0.8722 (mtt) cc_final: 0.8502 (mtm) REVERT: A 235 ILE cc_start: 0.9388 (pt) cc_final: 0.9171 (pt) REVERT: A 291 ARG cc_start: 0.8761 (ptt180) cc_final: 0.8548 (ptt-90) REVERT: C 80 ILE cc_start: 0.6303 (mp) cc_final: 0.6069 (mp) REVERT: C 129 MET cc_start: 0.8564 (ttm) cc_final: 0.8246 (mtm) REVERT: C 222 TYR cc_start: 0.8813 (t80) cc_final: 0.8499 (t80) REVERT: C 279 TYR cc_start: 0.8444 (p90) cc_final: 0.8206 (p90) REVERT: C 280 LYS cc_start: 0.8540 (tttt) cc_final: 0.7629 (tptt) REVERT: D 124 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7913 (mt-10) REVERT: D 216 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7738 (tp40) REVERT: D 279 TYR cc_start: 0.8755 (p90) cc_final: 0.8251 (p90) REVERT: D 291 ARG cc_start: 0.8412 (ptt180) cc_final: 0.7325 (ptt90) REVERT: D 293 LYS cc_start: 0.8370 (mttp) cc_final: 0.7904 (ttmm) REVERT: E 229 MET cc_start: 0.8980 (mtt) cc_final: 0.8778 (mtt) REVERT: B 229 MET cc_start: 0.8200 (mtt) cc_final: 0.7843 (mpp) REVERT: B 274 LYS cc_start: 0.9064 (mttt) cc_final: 0.8674 (mtmm) REVERT: B 280 LYS cc_start: 0.8293 (tttt) cc_final: 0.7791 (tptt) REVERT: B 290 SER cc_start: 0.7894 (t) cc_final: 0.7492 (t) outliers start: 24 outliers final: 7 residues processed: 388 average time/residue: 0.0845 time to fit residues: 48.0253 Evaluate side-chains 298 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 291 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 99 ASN H 60 ASN A 73 HIS A 176 ASN A 269 GLN C 71 ASN C 82 ASN C 216 GLN C 224 GLN C 245 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 224 GLN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN E 76 GLN E 82 ASN E 224 GLN B 76 GLN B 82 ASN B 245 HIS B 257 HIS B 276 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116694 restraints weight = 17377.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119351 restraints weight = 7665.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120931 restraints weight = 4224.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121845 restraints weight = 2806.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122324 restraints weight = 2186.265| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11074 Z= 0.151 Angle : 0.724 11.350 15045 Z= 0.375 Chirality : 0.048 0.268 1582 Planarity : 0.006 0.065 1927 Dihedral : 8.263 56.936 1555 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.59 % Favored : 92.03 % Rotamer: Outliers : 3.15 % Allowed : 16.88 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.49 % 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: -3.52 (0.20), residues: 1305 helix: -4.20 (0.25), residues: 113 sheet: -0.92 (0.26), residues: 354 loop : -2.89 (0.18), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 264 TYR 0.035 0.001 TYR H 80 PHE 0.010 0.001 PHE H 64 TRP 0.017 0.001 TRP D 261 HIS 0.003 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (11072) covalent geometry : angle 0.72417 / 0.37 (15041) SS BOND : bond 0.00487 / 0.25 ( 2) SS BOND : angle 1.02634 / 0.83 ( 4) hydrogen bonds : bond 0.04157 / 2.73 ( 202) hydrogen bonds : angle 5.95649 / 3.93 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.6015 (p90) cc_final: 0.5769 (p90) REVERT: H 33 TYR cc_start: 0.7571 (m-10) cc_final: 0.7311 (m-10) REVERT: H 57 ASP cc_start: 0.8308 (p0) cc_final: 0.7852 (p0) REVERT: H 59 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: A 119 LEU cc_start: 0.9491 (tt) cc_final: 0.9215 (tt) REVERT: A 167 ASP cc_start: 0.7941 (p0) cc_final: 0.7664 (p0) REVERT: A 272 LEU cc_start: 0.9253 (mt) cc_final: 0.9051 (mt) REVERT: C 191 SER cc_start: 0.8567 (m) cc_final: 0.8300 (t) REVERT: C 222 TYR cc_start: 0.8867 (t80) cc_final: 0.8536 (t80) REVERT: C 227 ASN cc_start: 0.8397 (p0) cc_final: 0.8160 (p0) REVERT: C 280 LYS cc_start: 0.8374 (tttt) cc_final: 0.7714 (tptt) REVERT: D 122 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8845 (ttpt) REVERT: D 124 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 167 ASP cc_start: 0.8050 (p0) cc_final: 0.7803 (p0) REVERT: D 183 MET cc_start: 0.8367 (mtp) cc_final: 0.7997 (mtm) REVERT: D 279 TYR cc_start: 0.8714 (p90) cc_final: 0.8135 (p90) REVERT: D 293 LYS cc_start: 0.8446 (mttp) cc_final: 0.8102 (tptp) REVERT: E 124 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8166 (mt-10) REVERT: E 153 TYR cc_start: 0.9395 (m-80) cc_final: 0.9144 (m-80) REVERT: E 222 TYR cc_start: 0.8772 (t80) cc_final: 0.8479 (t80) REVERT: E 229 MET cc_start: 0.8921 (mtt) cc_final: 0.8713 (mpp) REVERT: B 110 ASP cc_start: 0.8657 (t0) cc_final: 0.8436 (t0) REVERT: B 165 SER cc_start: 0.9467 (p) cc_final: 0.9263 (p) REVERT: B 229 MET cc_start: 0.8163 (mtt) cc_final: 0.7842 (mpp) REVERT: B 280 LYS cc_start: 0.8202 (tttt) cc_final: 0.7862 (tptt) REVERT: B 290 SER cc_start: 0.7960 (t) cc_final: 0.7568 (t) outliers start: 37 outliers final: 23 residues processed: 354 average time/residue: 0.0809 time to fit residues: 42.3937 Evaluate side-chains 337 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 313 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 4 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 99 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 62 GLN A 73 HIS A 82 ASN A 189 GLN A 278 ASN C 216 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN B 76 GLN B 82 ASN B 176 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112330 restraints weight = 17597.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114892 restraints weight = 7797.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116432 restraints weight = 4335.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117360 restraints weight = 2890.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.117841 restraints weight = 2255.306| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11074 Z= 0.198 Angle : 0.715 10.631 15045 Z= 0.366 Chirality : 0.048 0.255 1582 Planarity : 0.006 0.063 1927 Dihedral : 7.647 52.412 1541 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.66 % Favored : 91.95 % Rotamer: Outliers : 4.43 % Allowed : 18.58 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.33 % 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: -2.95 (0.21), residues: 1305 helix: -3.19 (0.40), residues: 97 sheet: -0.73 (0.26), residues: 370 loop : -2.53 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.030 0.002 TYR L 100 PHE 0.012 0.001 PHE L 104 TRP 0.013 0.001 TRP L 102 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11072) covalent geometry : angle 0.71465 / 0.37 (15041) SS BOND : bond 0.00403 / 0.20 ( 2) SS BOND : angle 1.16617 / 0.98 ( 4) hydrogen bonds : bond 0.03558 / 2.36 ( 202) hydrogen bonds : angle 5.45426 / 3.59 ( 765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.6166 (p90) cc_final: 0.5884 (p90) REVERT: H 33 TYR cc_start: 0.7667 (m-10) cc_final: 0.7413 (m-10) REVERT: H 39 GLN cc_start: 0.7823 (pp30) cc_final: 0.7083 (pp30) REVERT: H 57 ASP cc_start: 0.8427 (p0) cc_final: 0.7958 (p0) REVERT: H 83 LEU cc_start: 0.6978 (pt) cc_final: 0.6720 (pt) REVERT: A 167 ASP cc_start: 0.7942 (p0) cc_final: 0.7509 (p0) REVERT: A 280 LYS cc_start: 0.6950 (tptt) cc_final: 0.6254 (tptt) REVERT: C 110 ASP cc_start: 0.8916 (t0) cc_final: 0.8657 (t0) REVERT: C 122 LYS cc_start: 0.8802 (mtpt) cc_final: 0.7924 (mmtt) REVERT: C 129 MET cc_start: 0.8459 (mtp) cc_final: 0.8177 (mtm) REVERT: C 191 SER cc_start: 0.8961 (m) cc_final: 0.8759 (t) REVERT: C 206 ASP cc_start: 0.8232 (t0) cc_final: 0.7840 (t70) REVERT: C 222 TYR cc_start: 0.8877 (t80) cc_final: 0.8608 (t80) REVERT: C 280 LYS cc_start: 0.8445 (tttt) cc_final: 0.7746 (tptt) REVERT: D 122 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8908 (ttpt) REVERT: D 167 ASP cc_start: 0.8046 (p0) cc_final: 0.7801 (p0) REVERT: D 279 TYR cc_start: 0.8730 (p90) cc_final: 0.8179 (p90) REVERT: E 222 TYR cc_start: 0.8783 (t80) cc_final: 0.8507 (t80) REVERT: B 280 LYS cc_start: 0.8236 (tttt) cc_final: 0.7955 (tptt) outliers start: 52 outliers final: 39 residues processed: 349 average time/residue: 0.0826 time to fit residues: 43.2071 Evaluate side-chains 349 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 10.0000 chunk 127 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 61 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109528 restraints weight = 17434.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112123 restraints weight = 7521.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.113735 restraints weight = 4134.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114665 restraints weight = 2718.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115265 restraints weight = 2105.957| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11074 Z= 0.197 Angle : 0.711 10.781 15045 Z= 0.360 Chirality : 0.048 0.235 1582 Planarity : 0.005 0.063 1927 Dihedral : 7.509 50.403 1541 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.58 % Favored : 91.26 % Rotamer: Outliers : 5.29 % Allowed : 19.78 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.33 % 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: -2.55 (0.22), residues: 1305 helix: -2.63 (0.47), residues: 97 sheet: -0.34 (0.27), residues: 343 loop : -2.30 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 60 TYR 0.029 0.002 TYR L 100 PHE 0.013 0.001 PHE L 104 TRP 0.016 0.001 TRP L 56 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11072) covalent geometry : angle 0.71095 / 0.36 (15041) SS BOND : bond 0.00261 / 0.13 ( 2) SS BOND : angle 1.09716 / 0.99 ( 4) hydrogen bonds : bond 0.03250 / 2.14 ( 202) hydrogen bonds : angle 5.26552 / 3.46 ( 765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5199 (pp) REVERT: L 59 THR cc_start: 0.7187 (p) cc_final: 0.6986 (p) REVERT: H 32 TYR cc_start: 0.6169 (p90) cc_final: 0.5820 (p90) REVERT: H 33 TYR cc_start: 0.7703 (m-10) cc_final: 0.7396 (m-10) REVERT: H 34 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6494 (ttp) REVERT: H 39 GLN cc_start: 0.7844 (pp30) cc_final: 0.7001 (pp30) REVERT: H 46 GLU cc_start: 0.6839 (pm20) cc_final: 0.6601 (pm20) REVERT: H 57 ASP cc_start: 0.8506 (p0) cc_final: 0.7942 (p0) REVERT: H 83 LEU cc_start: 0.6994 (pt) cc_final: 0.6710 (pt) REVERT: A 167 ASP cc_start: 0.8088 (p0) cc_final: 0.7675 (p0) REVERT: A 280 LYS cc_start: 0.6937 (tptt) cc_final: 0.6433 (tptt) REVERT: C 71 ASN cc_start: 0.8254 (p0) cc_final: 0.7951 (p0) REVERT: C 110 ASP cc_start: 0.9017 (t0) cc_final: 0.8743 (t0) REVERT: C 122 LYS cc_start: 0.8932 (mtpt) cc_final: 0.7940 (mmtt) REVERT: C 129 MET cc_start: 0.8590 (mtp) cc_final: 0.8360 (mtm) REVERT: C 189 GLN cc_start: 0.8193 (mt0) cc_final: 0.7990 (tt0) REVERT: C 191 SER cc_start: 0.9053 (m) cc_final: 0.8829 (t) REVERT: C 206 ASP cc_start: 0.8397 (t0) cc_final: 0.8007 (t70) REVERT: C 216 GLN cc_start: 0.8636 (tp40) cc_final: 0.8297 (tp-100) REVERT: C 222 TYR cc_start: 0.9029 (t80) cc_final: 0.8765 (t80) REVERT: C 280 LYS cc_start: 0.8527 (tttt) cc_final: 0.7681 (tptt) REVERT: D 108 ASN cc_start: 0.8182 (t0) cc_final: 0.7802 (t0) REVERT: D 167 ASP cc_start: 0.8252 (p0) cc_final: 0.8047 (p0) REVERT: D 279 TYR cc_start: 0.8775 (p90) cc_final: 0.8225 (p90) REVERT: E 222 TYR cc_start: 0.8785 (t80) cc_final: 0.8515 (t80) REVERT: B 254 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8517 (ttp80) REVERT: B 274 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8991 (ttmt) REVERT: B 280 LYS cc_start: 0.8341 (tttt) cc_final: 0.7882 (tptt) outliers start: 62 outliers final: 47 residues processed: 351 average time/residue: 0.0813 time to fit residues: 42.6538 Evaluate side-chains 363 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.104940 restraints weight = 17538.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107423 restraints weight = 7801.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108902 restraints weight = 4336.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109841 restraints weight = 2887.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.110406 restraints weight = 2232.675| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.006 0.067 11074 Z= 0.264 Angle : 0.762 10.733 15045 Z= 0.385 Chirality : 0.050 0.260 1582 Planarity : 0.005 0.065 1927 Dihedral : 7.741 49.883 1541 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.12 % Favored : 90.65 % Rotamer: Outliers : 6.48 % Allowed : 19.86 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.16 % 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: -2.33 (0.22), residues: 1305 helix: -2.33 (0.50), residues: 97 sheet: -0.18 (0.28), residues: 340 loop : -2.16 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 120 TYR 0.032 0.002 TYR L 100 PHE 0.013 0.002 PHE L 104 TRP 0.017 0.002 TRP L 56 HIS 0.005 0.001 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.26 (11072) covalent geometry : angle 0.76202 / 0.38 (15041) SS BOND : bond 0.00207 / 0.10 ( 2) SS BOND : angle 1.28482 / 1.12 ( 4) hydrogen bonds : bond 0.03556 / 2.36 ( 202) hydrogen bonds : angle 5.32963 / 3.51 ( 765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 329 time to evaluate : 0.384 Fit side-chains REVERT: L 29 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5610 (pp) REVERT: L 59 THR cc_start: 0.7388 (p) cc_final: 0.7072 (p) REVERT: L 101 PRO cc_start: 0.5046 (Cg_endo) cc_final: 0.4816 (Cg_exo) REVERT: H 32 TYR cc_start: 0.6288 (p90) cc_final: 0.5945 (p90) REVERT: H 33 TYR cc_start: 0.7669 (m-10) cc_final: 0.7460 (m-10) REVERT: H 34 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6747 (ttp) REVERT: H 57 ASP cc_start: 0.8644 (p0) cc_final: 0.8048 (p0) REVERT: A 235 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9099 (pt) REVERT: A 280 LYS cc_start: 0.7009 (tptt) cc_final: 0.6459 (tptt) REVERT: C 122 LYS cc_start: 0.8868 (mtpt) cc_final: 0.7944 (mmtt) REVERT: C 129 MET cc_start: 0.8553 (mtp) cc_final: 0.8293 (mtm) REVERT: C 189 GLN cc_start: 0.8879 (mt0) cc_final: 0.8622 (tt0) REVERT: C 191 SER cc_start: 0.9083 (m) cc_final: 0.8871 (t) REVERT: C 206 ASP cc_start: 0.8521 (t0) cc_final: 0.8105 (t70) REVERT: C 216 GLN cc_start: 0.8702 (tp40) cc_final: 0.8330 (tp-100) REVERT: C 222 TYR cc_start: 0.9125 (t80) cc_final: 0.8424 (t80) REVERT: C 224 GLN cc_start: 0.9079 (mm110) cc_final: 0.8759 (mm110) REVERT: C 280 LYS cc_start: 0.8598 (tttt) cc_final: 0.7910 (tptt) REVERT: D 279 TYR cc_start: 0.8899 (p90) cc_final: 0.8170 (p90) REVERT: D 293 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7802 (tptp) REVERT: E 72 HIS cc_start: 0.8600 (m90) cc_final: 0.8289 (m-70) REVERT: B 110 ASP cc_start: 0.8971 (t0) cc_final: 0.8725 (t0) REVERT: B 141 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8735 (mtpt) REVERT: B 280 LYS cc_start: 0.8403 (tttt) cc_final: 0.8045 (tptt) outliers start: 76 outliers final: 57 residues processed: 367 average time/residue: 0.0844 time to fit residues: 45.9012 Evaluate side-chains 368 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 224 GLN C 278 ASN D 269 GLN D 282 ASN B 189 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109341 restraints weight = 17410.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.111880 restraints weight = 7642.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.113400 restraints weight = 4195.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114329 restraints weight = 2774.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114729 restraints weight = 2142.583| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11074 Z= 0.160 Angle : 0.700 10.274 15045 Z= 0.348 Chirality : 0.047 0.227 1582 Planarity : 0.005 0.063 1927 Dihedral : 7.370 49.784 1541 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer: Outliers : 4.94 % Allowed : 21.06 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.41 % 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: -2.14 (0.22), residues: 1305 helix: -2.20 (0.50), residues: 97 sheet: -0.13 (0.28), residues: 325 loop : -1.97 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.023 0.001 TYR H 80 PHE 0.013 0.001 PHE A 233 TRP 0.021 0.001 TRP L 56 HIS 0.002 0.001 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (11072) covalent geometry : angle 0.69972 / 0.35 (15041) SS BOND : bond 0.00214 / 0.11 ( 2) SS BOND : angle 1.08641 / 0.98 ( 4) hydrogen bonds : bond 0.03003 / 1.98 ( 202) hydrogen bonds : angle 5.09129 / 3.35 ( 765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 0.403 Fit side-chains REVERT: L 29 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5525 (pp) REVERT: L 59 THR cc_start: 0.7471 (p) cc_final: 0.7259 (p) REVERT: L 101 PRO cc_start: 0.4705 (Cg_endo) cc_final: 0.4434 (Cg_exo) REVERT: H 32 TYR cc_start: 0.6069 (p90) cc_final: 0.5800 (p90) REVERT: H 46 GLU cc_start: 0.6957 (pm20) cc_final: 0.6652 (pm20) REVERT: A 224 GLN cc_start: 0.8844 (mm110) cc_final: 0.8499 (mm-40) REVERT: A 235 ILE cc_start: 0.9359 (pt) cc_final: 0.9128 (pt) REVERT: A 280 LYS cc_start: 0.6941 (tptt) cc_final: 0.6273 (tptt) REVERT: C 189 GLN cc_start: 0.8167 (mt0) cc_final: 0.7907 (tt0) REVERT: C 206 ASP cc_start: 0.8444 (t0) cc_final: 0.7996 (t70) REVERT: C 216 GLN cc_start: 0.8665 (tp40) cc_final: 0.8248 (tp-100) REVERT: C 222 TYR cc_start: 0.9036 (t80) cc_final: 0.8517 (t80) REVERT: C 280 LYS cc_start: 0.8572 (tttt) cc_final: 0.7858 (tptt) REVERT: D 108 ASN cc_start: 0.8188 (t0) cc_final: 0.7952 (t0) REVERT: D 279 TYR cc_start: 0.8771 (p90) cc_final: 0.8136 (p90) REVERT: D 293 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7804 (tptp) REVERT: E 72 HIS cc_start: 0.8604 (m90) cc_final: 0.8292 (m-70) outliers start: 58 outliers final: 47 residues processed: 346 average time/residue: 0.0802 time to fit residues: 41.4045 Evaluate side-chains 361 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 278 ASN D 269 GLN E 176 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108753 restraints weight = 17237.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.111304 restraints weight = 7628.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.112807 restraints weight = 4207.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.113729 restraints weight = 2803.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114308 restraints weight = 2181.147| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11074 Z= 0.169 Angle : 0.712 10.124 15045 Z= 0.352 Chirality : 0.047 0.303 1582 Planarity : 0.005 0.060 1927 Dihedral : 7.248 48.966 1541 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.80 % Rotamer: Outliers : 5.20 % Allowed : 21.14 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % 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: -2.07 (0.23), residues: 1305 helix: -2.11 (0.50), residues: 97 sheet: -0.13 (0.28), residues: 325 loop : -1.89 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.015 0.002 TYR E 106 PHE 0.012 0.001 PHE B 233 TRP 0.026 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (11072) covalent geometry : angle 0.71144 / 0.35 (15041) SS BOND : bond 0.00149 / 0.08 ( 2) SS BOND : angle 1.07500 / 0.99 ( 4) hydrogen bonds : bond 0.02970 / 1.95 ( 202) hydrogen bonds : angle 5.06647 / 3.33 ( 765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 0.417 Fit side-chains REVERT: L 29 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5649 (pp) REVERT: L 95 GLN cc_start: 0.5563 (OUTLIER) cc_final: 0.5195 (pt0) REVERT: L 101 PRO cc_start: 0.4830 (Cg_endo) cc_final: 0.4555 (Cg_exo) REVERT: H 32 TYR cc_start: 0.6185 (p90) cc_final: 0.5968 (p90) REVERT: H 46 GLU cc_start: 0.6934 (pm20) cc_final: 0.6638 (pm20) REVERT: A 224 GLN cc_start: 0.8851 (mm110) cc_final: 0.8485 (mm-40) REVERT: A 235 ILE cc_start: 0.9362 (pt) cc_final: 0.9101 (pt) REVERT: A 280 LYS cc_start: 0.6979 (tptt) cc_final: 0.6484 (tptt) REVERT: C 95 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7772 (mtp) REVERT: C 189 GLN cc_start: 0.8833 (mt0) cc_final: 0.8575 (tt0) REVERT: C 206 ASP cc_start: 0.8404 (t0) cc_final: 0.7939 (t70) REVERT: C 216 GLN cc_start: 0.8665 (tp40) cc_final: 0.8221 (tp-100) REVERT: C 222 TYR cc_start: 0.9036 (t80) cc_final: 0.8677 (t80) REVERT: C 280 LYS cc_start: 0.8623 (tttt) cc_final: 0.7858 (tptt) REVERT: D 279 TYR cc_start: 0.8738 (p90) cc_final: 0.8221 (p90) REVERT: D 293 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7804 (tptp) REVERT: E 72 HIS cc_start: 0.8669 (m90) cc_final: 0.8399 (m-70) REVERT: E 183 MET cc_start: 0.8778 (ttm) cc_final: 0.7881 (mtp) outliers start: 61 outliers final: 51 residues processed: 353 average time/residue: 0.0800 time to fit residues: 42.0380 Evaluate side-chains 372 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109565 restraints weight = 17390.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.112070 restraints weight = 7721.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113550 restraints weight = 4294.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.114441 restraints weight = 2857.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114972 restraints weight = 2233.381| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11074 Z= 0.189 Angle : 0.719 10.757 15045 Z= 0.357 Chirality : 0.048 0.271 1582 Planarity : 0.005 0.061 1927 Dihedral : 7.225 48.698 1541 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.58 % Favored : 90.27 % Rotamer: Outliers : 5.63 % Allowed : 21.06 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.16 % 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: -1.97 (0.23), residues: 1305 helix: -2.04 (0.51), residues: 97 sheet: -0.10 (0.29), residues: 325 loop : -1.81 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.014 0.002 TYR E 106 PHE 0.011 0.001 PHE B 233 TRP 0.020 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (11072) covalent geometry : angle 0.71887 / 0.36 (15041) SS BOND : bond 0.00117 / 0.06 ( 2) SS BOND : angle 1.10087 / 1.00 ( 4) hydrogen bonds : bond 0.03035 / 1.99 ( 202) hydrogen bonds : angle 5.05199 / 3.31 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5682 (pp) REVERT: L 95 GLN cc_start: 0.5821 (pt0) cc_final: 0.5493 (pt0) REVERT: L 101 PRO cc_start: 0.4940 (Cg_endo) cc_final: 0.4645 (Cg_exo) REVERT: H 46 GLU cc_start: 0.6914 (pm20) cc_final: 0.6620 (pm20) REVERT: H 57 ASP cc_start: 0.8729 (p0) cc_final: 0.7774 (p0) REVERT: A 224 GLN cc_start: 0.8864 (mm110) cc_final: 0.8483 (mm-40) REVERT: A 235 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9101 (pt) REVERT: A 280 LYS cc_start: 0.7004 (tptt) cc_final: 0.6444 (tptt) REVERT: C 95 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: C 189 GLN cc_start: 0.8849 (mt0) cc_final: 0.8562 (tt0) REVERT: C 206 ASP cc_start: 0.8373 (t0) cc_final: 0.7931 (t70) REVERT: C 213 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8239 (mm-30) REVERT: C 216 GLN cc_start: 0.8657 (tp40) cc_final: 0.8200 (tp-100) REVERT: C 222 TYR cc_start: 0.9056 (t80) cc_final: 0.8718 (t80) REVERT: C 280 LYS cc_start: 0.8584 (tttt) cc_final: 0.7865 (tptt) REVERT: D 271 TYR cc_start: 0.9416 (m-80) cc_final: 0.9188 (m-80) REVERT: D 279 TYR cc_start: 0.8780 (p90) cc_final: 0.8236 (p90) REVERT: D 293 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7878 (tptp) REVERT: E 72 HIS cc_start: 0.8651 (m90) cc_final: 0.8376 (m-70) REVERT: E 183 MET cc_start: 0.8736 (ttm) cc_final: 0.7809 (mtp) outliers start: 66 outliers final: 54 residues processed: 354 average time/residue: 0.0813 time to fit residues: 42.7798 Evaluate side-chains 371 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 128 optimal weight: 0.0030 chunk 70 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 176 ASN E 189 GLN B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.128658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110097 restraints weight = 17293.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112544 restraints weight = 7718.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.114067 restraints weight = 4300.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114952 restraints weight = 2870.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115515 restraints weight = 2242.745| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11074 Z= 0.147 Angle : 0.701 9.604 15045 Z= 0.345 Chirality : 0.047 0.213 1582 Planarity : 0.005 0.061 1927 Dihedral : 7.045 47.695 1541 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.80 % Rotamer: Outliers : 4.69 % Allowed : 22.42 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % 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: -1.85 (0.23), residues: 1305 helix: -1.98 (0.51), residues: 97 sheet: -0.03 (0.29), residues: 325 loop : -1.71 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.013 0.001 TYR E 106 PHE 0.012 0.001 PHE B 233 TRP 0.024 0.001 TRP L 56 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (11072) covalent geometry : angle 0.70102 / 0.35 (15041) SS BOND : bond 0.00113 / 0.06 ( 2) SS BOND : angle 0.99920 / 0.92 ( 4) hydrogen bonds : bond 0.02802 / 1.83 ( 202) hydrogen bonds : angle 4.92992 / 3.23 ( 765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5544 (pp) REVERT: L 101 PRO cc_start: 0.4894 (Cg_endo) cc_final: 0.4587 (Cg_exo) REVERT: H 46 GLU cc_start: 0.6902 (pm20) cc_final: 0.6599 (pm20) REVERT: H 57 ASP cc_start: 0.8742 (p0) cc_final: 0.7610 (p0) REVERT: A 224 GLN cc_start: 0.8853 (mm110) cc_final: 0.8448 (mm-40) REVERT: A 235 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9123 (pt) REVERT: A 280 LYS cc_start: 0.6860 (tptt) cc_final: 0.6253 (tptt) REVERT: C 95 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: C 189 GLN cc_start: 0.8836 (mt0) cc_final: 0.8585 (tt0) REVERT: C 206 ASP cc_start: 0.8312 (t0) cc_final: 0.7845 (t70) REVERT: C 213 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 222 TYR cc_start: 0.9034 (t80) cc_final: 0.8803 (t80) REVERT: C 280 LYS cc_start: 0.8526 (tttt) cc_final: 0.7779 (tptt) REVERT: D 279 TYR cc_start: 0.8660 (p90) cc_final: 0.8150 (p90) REVERT: D 293 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7877 (tptp) REVERT: E 72 HIS cc_start: 0.8644 (m90) cc_final: 0.8374 (m-70) REVERT: E 183 MET cc_start: 0.8679 (ttm) cc_final: 0.7810 (mtp) outliers start: 55 outliers final: 47 residues processed: 354 average time/residue: 0.0808 time to fit residues: 42.9100 Evaluate side-chains 371 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 321 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 122 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 95 GLN H 5 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.113815 restraints weight = 17287.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116428 restraints weight = 7457.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117981 restraints weight = 4082.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118857 restraints weight = 2693.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119216 restraints weight = 2111.257| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11074 Z= 0.122 Angle : 0.690 10.020 15045 Z= 0.338 Chirality : 0.046 0.210 1582 Planarity : 0.005 0.058 1927 Dihedral : 6.854 46.590 1541 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.03 % Rotamer: Outliers : 3.92 % Allowed : 23.79 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.16 % 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: -1.70 (0.23), residues: 1305 helix: -1.86 (0.51), residues: 97 sheet: 0.07 (0.29), residues: 325 loop : -1.61 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.012 0.001 TYR E 106 PHE 0.012 0.001 PHE B 233 TRP 0.022 0.001 TRP L 56 HIS 0.005 0.000 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (11072) covalent geometry : angle 0.68976 / 0.34 (15041) SS BOND : bond 0.00064 / 0.03 ( 2) SS BOND : angle 1.17779 / 1.00 ( 4) hydrogen bonds : bond 0.02654 / 1.70 ( 202) hydrogen bonds : angle 4.79426 / 3.13 ( 765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.347 Fit side-chains REVERT: L 29 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5195 (pp) REVERT: H 35 LYS cc_start: 0.8362 (mppt) cc_final: 0.8011 (mptt) REVERT: H 46 GLU cc_start: 0.6871 (pm20) cc_final: 0.6561 (pm20) REVERT: H 57 ASP cc_start: 0.8755 (p0) cc_final: 0.7632 (p0) REVERT: A 106 TYR cc_start: 0.8988 (p90) cc_final: 0.8603 (p90) REVERT: A 224 GLN cc_start: 0.8783 (mm110) cc_final: 0.8384 (mm-40) REVERT: A 235 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9100 (pt) REVERT: A 280 LYS cc_start: 0.6750 (tptt) cc_final: 0.6110 (tptt) REVERT: C 95 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8281 (mtp) REVERT: C 189 GLN cc_start: 0.8814 (mt0) cc_final: 0.8600 (tt0) REVERT: C 206 ASP cc_start: 0.8343 (t0) cc_final: 0.7852 (t70) REVERT: C 213 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8216 (mm-30) REVERT: C 222 TYR cc_start: 0.9031 (t80) cc_final: 0.8734 (t80) REVERT: C 280 LYS cc_start: 0.8509 (tttt) cc_final: 0.7660 (tptt) REVERT: D 108 ASN cc_start: 0.8070 (t0) cc_final: 0.7820 (t0) REVERT: D 279 TYR cc_start: 0.8628 (p90) cc_final: 0.8163 (p90) REVERT: D 293 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7800 (tptp) REVERT: E 72 HIS cc_start: 0.8657 (m90) cc_final: 0.8401 (m-70) REVERT: E 111 ILE cc_start: 0.9059 (mt) cc_final: 0.8851 (mt) REVERT: E 183 MET cc_start: 0.8617 (ttm) cc_final: 0.7810 (mtp) outliers start: 46 outliers final: 36 residues processed: 347 average time/residue: 0.0809 time to fit residues: 42.3423 Evaluate side-chains 350 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.113385 restraints weight = 17391.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115981 restraints weight = 7497.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117580 restraints weight = 4097.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118531 restraints weight = 2693.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119097 restraints weight = 2084.448| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11074 Z= 0.144 Angle : 0.696 9.297 15045 Z= 0.343 Chirality : 0.047 0.212 1582 Planarity : 0.005 0.060 1927 Dihedral : 6.830 45.529 1541 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.97 % Favored : 90.88 % Rotamer: Outliers : 3.75 % Allowed : 23.79 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % 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: -1.61 (0.23), residues: 1305 helix: -1.75 (0.53), residues: 97 sheet: 0.10 (0.29), residues: 325 loop : -1.54 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.022 0.001 TYR A 128 PHE 0.011 0.001 PHE B 233 TRP 0.024 0.001 TRP L 56 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.14 (11072) covalent geometry : angle 0.69582 / 0.34 (15041) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 1.04795 / 0.94 ( 4) hydrogen bonds : bond 0.02782 / 1.80 ( 202) hydrogen bonds : angle 4.79547 / 3.13 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.67 seconds wall clock time: 32 minutes 15.45 seconds (1935.45 seconds total)