Starting phenix.real_space_refine on Wed Mar 4 03:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lht_0897/03_2026/6lht_0897.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lht_0897/03_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_0897/03_2026/6lht_0897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lht_0897/03_2026/6lht_0897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lht_0897/03_2026/6lht_0897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lht_0897/03_2026/6lht_0897.map" } 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-dev-5986/lib/python3.9/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: 2.16, per 1000 atoms: 0.20 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: 0.63 Conformation dependent library (CDL) restraints added in 435.7 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: 0.30 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: 1.43 Time building geometry restraints manager: 0.92 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=" C4 SPH E 301 " pdb=" C5 SPH E 301 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C4 SPH B 301 " pdb=" C5 SPH B 301 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C4 SPH D 301 " pdb=" C5 SPH D 301 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 SPH C 301 " pdb=" C5 SPH C 301 " ideal model delta sigma weight residual 1.334 1.466 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 11067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 14934 5.34 - 10.68: 92 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: 5815 17.98 - 35.95: 615 35.95 - 53.93: 133 53.93 - 71.91: 35 71.91 - 89.88: 13 Dihedral angle restraints: 6611 sinusoidal: 2714 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 6608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1512 0.132 - 0.263: 61 0.263 - 0.395: 16 0.395 - 0.527: 2 0.527 - 0.658: 1 Chirality restraints: 1592 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 1589 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH C 301 " -0.231 2.00e-02 2.50e+03 2.29e-01 5.24e+02 pdb=" C4 SPH C 301 " 0.232 2.00e-02 2.50e+03 pdb=" C5 SPH C 301 " 0.226 2.00e-02 2.50e+03 pdb=" C6 SPH C 301 " -0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SPH B 301 " -0.230 2.00e-02 2.50e+03 2.29e-01 5.23e+02 pdb=" C4 SPH B 301 " 0.232 2.00e-02 2.50e+03 pdb=" C5 SPH B 301 " 0.225 2.00e-02 2.50e+03 pdb=" C6 SPH B 301 " -0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " -0.231 2.00e-02 2.50e+03 2.29e-01 5.23e+02 pdb=" C4 SPH A 301 " 0.232 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " 0.225 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " -0.227 2.00e-02 2.50e+03 ... (remaining 1929 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: 0.150 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 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: 0.8047 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 : 0.008 0.133 11074 Z= 0.434 Angle : 1.155 26.699 15045 Z= 0.650 Chirality : 0.072 0.658 1592 Planarity : 0.015 0.229 1932 Dihedral : 15.819 89.881 4103 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 covalent geometry : bond 0.00795 (11072) covalent geometry : angle 1.15421 (15041) SS BOND : bond 0.01375 ( 2) SS BOND : angle 2.82795 ( 4) hydrogen bonds : bond 0.27681 ( 202) hydrogen bonds : angle 10.58894 ( 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 : 0.304 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: 0.0828 time to fit residues: 47.0307 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 : 0.289 ------------------------------------------------------------------------------- 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: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN H 60 ASN H 62 GLN 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 176 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.134354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115819 restraints weight = 17351.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118477 restraints weight = 7672.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119915 restraints weight = 4245.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120975 restraints weight = 2868.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121510 restraints weight = 2208.666| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11074 Z= 0.145 Angle : 0.716 11.081 15045 Z= 0.370 Chirality : 0.047 0.272 1592 Planarity : 0.006 0.065 1932 Dihedral : 9.933 57.885 1575 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.43 % Favored : 92.18 % Rotamer: Outliers : 2.98 % Allowed : 16.97 % Favored : 80.05 % 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: -3.53 (0.20), residues: 1305 helix: -4.22 (0.23), residues: 117 sheet: -0.92 (0.27), residues: 354 loop : -2.88 (0.18), residues: 834 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 0.011 0.001 PHE H 64 TRP 0.017 0.001 TRP D 261 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00329 (11072) covalent geometry : angle 0.71640 (15041) SS BOND : bond 0.00461 ( 2) SS BOND : angle 1.01404 ( 4) hydrogen bonds : bond 0.04500 ( 202) hydrogen bonds : angle 5.99658 ( 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 371 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 59 THR cc_start: 0.7377 (p) cc_final: 0.7154 (p) REVERT: H 32 TYR cc_start: 0.5966 (p90) cc_final: 0.5718 (p90) REVERT: H 33 TYR cc_start: 0.7575 (m-10) cc_final: 0.7311 (m-10) REVERT: H 39 GLN cc_start: 0.7646 (pp30) cc_final: 0.6885 (pp30) REVERT: H 57 ASP cc_start: 0.8247 (p0) cc_final: 0.7904 (p0) REVERT: H 59 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 119 LEU cc_start: 0.9487 (tt) cc_final: 0.9200 (tt) REVERT: A 167 ASP cc_start: 0.7935 (p0) cc_final: 0.7650 (p0) REVERT: A 280 LYS cc_start: 0.6472 (tptt) cc_final: 0.5856 (tptt) REVERT: C 191 SER cc_start: 0.8555 (m) cc_final: 0.8296 (t) REVERT: C 222 TYR cc_start: 0.8856 (t80) cc_final: 0.8523 (t80) REVERT: C 227 ASN cc_start: 0.8374 (p0) cc_final: 0.8158 (p0) REVERT: C 280 LYS cc_start: 0.8347 (tttt) cc_final: 0.7692 (tptt) REVERT: D 124 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 167 ASP cc_start: 0.8043 (p0) cc_final: 0.7770 (p0) REVERT: D 183 MET cc_start: 0.8372 (mtp) cc_final: 0.7997 (mtm) REVERT: D 279 TYR cc_start: 0.8704 (p90) cc_final: 0.8143 (p90) REVERT: D 293 LYS cc_start: 0.8433 (mttp) cc_final: 0.8115 (tptp) REVERT: E 106 TYR cc_start: 0.8925 (p90) cc_final: 0.8712 (p90) REVERT: E 124 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8154 (mt-10) REVERT: E 153 TYR cc_start: 0.9389 (m-80) cc_final: 0.9139 (m-80) REVERT: E 222 TYR cc_start: 0.8759 (t80) cc_final: 0.8478 (t80) REVERT: E 229 MET cc_start: 0.8897 (mtt) cc_final: 0.8695 (mpp) REVERT: B 110 ASP cc_start: 0.8645 (t0) cc_final: 0.8424 (t0) REVERT: B 165 SER cc_start: 0.9461 (p) cc_final: 0.9260 (p) REVERT: B 229 MET cc_start: 0.8134 (mtt) cc_final: 0.7846 (mpp) REVERT: B 280 LYS cc_start: 0.8181 (tttt) cc_final: 0.7852 (tptt) REVERT: B 290 SER cc_start: 0.7944 (t) cc_final: 0.7551 (t) outliers start: 35 outliers final: 22 residues processed: 350 average time/residue: 0.0800 time to fit residues: 41.7949 Evaluate side-chains 337 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 91 SER 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: 7.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS A 82 ASN A 189 GLN A 278 ASN C 216 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 216 GLN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 82 ASN B 176 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.109782 restraints weight = 17628.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112323 restraints weight = 7839.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113822 restraints weight = 4371.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114689 restraints weight = 2925.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115268 restraints weight = 2305.888| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11074 Z= 0.244 Angle : 0.747 10.711 15045 Z= 0.384 Chirality : 0.049 0.263 1592 Planarity : 0.006 0.064 1932 Dihedral : 9.046 59.617 1561 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.28 % Favored : 91.34 % Rotamer: Outliers : 4.77 % Allowed : 18.07 % Favored : 77.15 % 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: -2.95 (0.21), residues: 1305 helix: -3.15 (0.41), residues: 97 sheet: -0.76 (0.27), residues: 360 loop : -2.51 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 264 TYR 0.034 0.002 TYR L 100 PHE 0.013 0.002 PHE L 104 TRP 0.014 0.002 TRP L 102 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00594 (11072) covalent geometry : angle 0.74673 (15041) SS BOND : bond 0.00417 ( 2) SS BOND : angle 1.28158 ( 4) hydrogen bonds : bond 0.03814 ( 202) hydrogen bonds : angle 5.53723 ( 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 386 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 330 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 LEU cc_start: 0.6578 (tp) cc_final: 0.6376 (tp) REVERT: H 32 TYR cc_start: 0.6275 (p90) cc_final: 0.5960 (p90) REVERT: H 33 TYR cc_start: 0.7728 (m-10) cc_final: 0.7417 (m-10) REVERT: H 38 LYS cc_start: 0.7479 (ttpp) cc_final: 0.7152 (ttpp) REVERT: H 39 GLN cc_start: 0.7888 (pp30) cc_final: 0.7109 (pp30) REVERT: H 57 ASP cc_start: 0.8443 (p0) cc_final: 0.7871 (p0) REVERT: H 83 LEU cc_start: 0.6859 (pt) cc_final: 0.6541 (pt) REVERT: A 201 TYR cc_start: 0.9186 (m-80) cc_final: 0.8974 (m-80) REVERT: A 280 LYS cc_start: 0.6745 (tptt) cc_final: 0.6063 (tptt) REVERT: C 110 ASP cc_start: 0.8974 (t0) cc_final: 0.8687 (t0) REVERT: C 122 LYS cc_start: 0.8815 (mtpt) cc_final: 0.7899 (mmtt) REVERT: C 129 MET cc_start: 0.8488 (mtp) cc_final: 0.8181 (mtm) REVERT: C 191 SER cc_start: 0.9007 (m) cc_final: 0.8783 (t) REVERT: C 206 ASP cc_start: 0.8279 (t0) cc_final: 0.7895 (t70) REVERT: C 222 TYR cc_start: 0.8918 (t80) cc_final: 0.8672 (t80) REVERT: C 280 LYS cc_start: 0.8552 (tttt) cc_final: 0.7819 (tptt) REVERT: C 283 ASP cc_start: 0.7852 (t70) cc_final: 0.7625 (t0) REVERT: D 167 ASP cc_start: 0.8181 (p0) cc_final: 0.7978 (p0) REVERT: D 183 MET cc_start: 0.8570 (mtp) cc_final: 0.8352 (mtm) REVERT: D 279 TYR cc_start: 0.8804 (p90) cc_final: 0.8582 (p90) REVERT: E 106 TYR cc_start: 0.9147 (p90) cc_final: 0.8839 (p90) REVERT: E 222 TYR cc_start: 0.8816 (t80) cc_final: 0.8524 (t80) REVERT: E 229 MET cc_start: 0.9104 (mtt) cc_final: 0.8783 (mtt) REVERT: B 229 MET cc_start: 0.8257 (mtt) cc_final: 0.7923 (mpp) REVERT: B 280 LYS cc_start: 0.8327 (tttt) cc_final: 0.7999 (tptt) outliers start: 56 outliers final: 44 residues processed: 356 average time/residue: 0.0911 time to fit residues: 47.7653 Evaluate side-chains 361 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 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 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 D residue 294 ILE Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS 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 210 THR 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 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: 3.9990 chunk 127 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 50.0000 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3351 r_free = 0.3351 target = 0.129408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.110802 restraints weight = 17326.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.113374 restraints weight = 7648.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114926 restraints weight = 4231.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115878 restraints weight = 2810.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116415 restraints weight = 2181.609| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11074 Z= 0.154 Angle : 0.692 10.692 15045 Z= 0.348 Chirality : 0.047 0.230 1592 Planarity : 0.005 0.062 1932 Dihedral : 8.410 59.969 1561 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.66 % Favored : 92.18 % Rotamer: Outliers : 4.77 % Allowed : 19.35 % Favored : 75.87 % Cbeta Deviations : 0.00 % 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: -2.57 (0.22), residues: 1305 helix: -2.71 (0.45), residues: 97 sheet: -0.33 (0.27), residues: 351 loop : -2.33 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 60 TYR 0.027 0.001 TYR L 100 PHE 0.012 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 covalent geometry : bond 0.00372 (11072) covalent geometry : angle 0.69195 (15041) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.97130 ( 4) hydrogen bonds : bond 0.03000 ( 202) hydrogen bonds : angle 5.16451 ( 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 384 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 328 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5513 (pp) REVERT: L 59 THR cc_start: 0.7287 (p) cc_final: 0.7043 (p) REVERT: H 32 TYR cc_start: 0.6047 (p90) cc_final: 0.5778 (p90) REVERT: H 33 TYR cc_start: 0.7666 (m-10) cc_final: 0.7391 (m-10) REVERT: H 39 GLN cc_start: 0.7811 (pp30) cc_final: 0.6989 (pp30) REVERT: H 57 ASP cc_start: 0.8356 (p0) cc_final: 0.7815 (p0) REVERT: H 83 LEU cc_start: 0.6883 (pt) cc_final: 0.6633 (pt) REVERT: A 167 ASP cc_start: 0.7967 (p0) cc_final: 0.7555 (p0) REVERT: A 280 LYS cc_start: 0.6729 (tptt) cc_final: 0.6242 (tptt) REVERT: C 71 ASN cc_start: 0.8023 (p0) cc_final: 0.7683 (p0) REVERT: C 110 ASP cc_start: 0.8957 (t0) cc_final: 0.8675 (t0) REVERT: C 122 LYS cc_start: 0.8866 (mtpt) cc_final: 0.7925 (mmtt) REVERT: C 129 MET cc_start: 0.8488 (mtp) cc_final: 0.8254 (mtm) REVERT: C 191 SER cc_start: 0.9041 (m) cc_final: 0.8838 (t) REVERT: C 206 ASP cc_start: 0.8362 (t0) cc_final: 0.7941 (t70) REVERT: C 216 GLN cc_start: 0.8573 (tp40) cc_final: 0.8243 (tp-100) REVERT: C 222 TYR cc_start: 0.8974 (t80) cc_final: 0.8647 (t80) REVERT: C 280 LYS cc_start: 0.8473 (tttt) cc_final: 0.7690 (tptt) REVERT: D 167 ASP cc_start: 0.8130 (p0) cc_final: 0.7911 (p0) REVERT: D 183 MET cc_start: 0.8598 (mtp) cc_final: 0.8335 (mtm) REVERT: D 271 TYR cc_start: 0.9445 (m-80) cc_final: 0.9229 (m-80) REVERT: D 279 TYR cc_start: 0.8714 (p90) cc_final: 0.8225 (p90) REVERT: E 124 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8309 (mt-10) REVERT: E 222 TYR cc_start: 0.8814 (t80) cc_final: 0.8561 (t80) REVERT: E 229 MET cc_start: 0.8958 (mtt) cc_final: 0.8719 (mtt) REVERT: B 229 MET cc_start: 0.8162 (mtt) cc_final: 0.7881 (mpp) REVERT: B 280 LYS cc_start: 0.8273 (tttt) cc_final: 0.7885 (tptt) outliers start: 56 outliers final: 44 residues processed: 350 average time/residue: 0.0855 time to fit residues: 44.4842 Evaluate side-chains 359 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 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 178 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 91 SER 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 D residue 146 LEU 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 287 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 139 VAL 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 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 Chi-restraints excluded: chain B residue 275 THR 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: 10.0000 chunk 36 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** E 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 = 0.3262 r_free = 0.3262 target = 0.122813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.104356 restraints weight = 17690.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106897 restraints weight = 7717.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108445 restraints weight = 4247.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109356 restraints weight = 2791.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109936 restraints weight = 2158.664| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 11074 Z= 0.315 Angle : 0.798 11.207 15045 Z= 0.404 Chirality : 0.051 0.271 1592 Planarity : 0.006 0.065 1932 Dihedral : 8.678 59.786 1561 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.19 % Favored : 89.58 % Rotamer: Outliers : 6.48 % Allowed : 19.52 % Favored : 74.00 % 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: -2.41 (0.22), residues: 1305 helix: -2.32 (0.51), residues: 97 sheet: -0.28 (0.28), residues: 343 loop : -2.22 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 120 TYR 0.034 0.002 TYR L 100 PHE 0.014 0.002 PHE L 104 TRP 0.016 0.002 TRP L 56 HIS 0.005 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00767 (11072) covalent geometry : angle 0.79747 (15041) SS BOND : bond 0.00278 ( 2) SS BOND : angle 1.40940 ( 4) hydrogen bonds : bond 0.03775 ( 202) hydrogen bonds : angle 5.45264 ( 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 396 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 320 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5565 (pp) REVERT: L 59 THR cc_start: 0.7603 (p) cc_final: 0.7282 (p) REVERT: L 101 PRO cc_start: 0.5253 (Cg_endo) cc_final: 0.4995 (Cg_exo) REVERT: H 32 TYR cc_start: 0.6382 (p90) cc_final: 0.5986 (p90) REVERT: H 33 TYR cc_start: 0.7707 (m-10) cc_final: 0.7461 (m-10) REVERT: H 57 ASP cc_start: 0.8734 (p0) cc_final: 0.8156 (p0) REVERT: A 205 TYR cc_start: 0.8745 (t80) cc_final: 0.8502 (t80) REVERT: A 224 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8532 (mm-40) REVERT: A 235 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9061 (pt) REVERT: A 280 LYS cc_start: 0.6876 (tptt) cc_final: 0.6314 (tptt) REVERT: C 122 LYS cc_start: 0.8959 (mtpt) cc_final: 0.7969 (mmtt) REVERT: C 129 MET cc_start: 0.8605 (mtp) cc_final: 0.8317 (mtm) REVERT: C 189 GLN cc_start: 0.8913 (mt0) cc_final: 0.8581 (tt0) REVERT: C 206 ASP cc_start: 0.8470 (t0) cc_final: 0.8127 (t70) REVERT: C 216 GLN cc_start: 0.8659 (tp40) cc_final: 0.8295 (tp-100) REVERT: C 224 GLN cc_start: 0.9082 (mm110) cc_final: 0.8717 (mm110) REVERT: C 280 LYS cc_start: 0.8651 (tttt) cc_final: 0.7865 (tptt) REVERT: D 279 TYR cc_start: 0.8952 (p90) cc_final: 0.8185 (p90) REVERT: D 280 LYS cc_start: 0.8006 (tttt) cc_final: 0.7771 (tptt) REVERT: D 293 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7717 (tptp) REVERT: E 222 TYR cc_start: 0.8808 (t80) cc_final: 0.8591 (t80) REVERT: E 229 MET cc_start: 0.9022 (mtt) cc_final: 0.8763 (mtt) REVERT: B 110 ASP cc_start: 0.8987 (t0) cc_final: 0.8717 (t0) REVERT: B 229 MET cc_start: 0.8396 (mtt) cc_final: 0.7901 (mpp) REVERT: B 280 LYS cc_start: 0.8388 (tttt) cc_final: 0.7940 (tptt) outliers start: 76 outliers final: 62 residues processed: 358 average time/residue: 0.0906 time to fit residues: 47.3123 Evaluate side-chains 372 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 111 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 LEU 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 C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 190 VAL 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 129 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 189 GLN 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 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS 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 210 THR 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 Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 224 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3336 r_free = 0.3336 target = 0.128362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.110004 restraints weight = 17407.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112528 restraints weight = 7659.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.113912 restraints weight = 4218.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114951 restraints weight = 2840.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.115380 restraints weight = 2189.103| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3629 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= 0.159 Angle : 0.696 10.320 15045 Z= 0.348 Chirality : 0.047 0.226 1592 Planarity : 0.005 0.065 1932 Dihedral : 8.348 59.106 1561 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.12 % Favored : 91.65 % Rotamer: Outliers : 5.12 % Allowed : 21.23 % Favored : 73.66 % 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: -2.27 (0.22), residues: 1305 helix: -2.13 (0.51), residues: 97 sheet: -0.22 (0.28), residues: 325 loop : -2.08 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.024 0.001 TYR H 80 PHE 0.012 0.001 PHE L 104 TRP 0.023 0.001 TRP L 56 HIS 0.002 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00390 (11072) covalent geometry : angle 0.69595 (15041) SS BOND : bond 0.00221 ( 2) SS BOND : angle 1.05945 ( 4) hydrogen bonds : bond 0.02998 ( 202) hydrogen bonds : angle 5.13712 ( 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 381 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5504 (pp) REVERT: L 53 LEU cc_start: 0.8934 (mt) cc_final: 0.8718 (mt) REVERT: L 59 THR cc_start: 0.7596 (p) cc_final: 0.7384 (p) REVERT: H 32 TYR cc_start: 0.6102 (p90) cc_final: 0.5825 (p90) REVERT: H 34 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6769 (ttp) REVERT: A 205 TYR cc_start: 0.8713 (t80) cc_final: 0.8477 (t80) REVERT: A 224 GLN cc_start: 0.8965 (mm110) cc_final: 0.8583 (mm-40) REVERT: A 280 LYS cc_start: 0.6891 (tptt) cc_final: 0.6292 (tptt) REVERT: C 189 GLN cc_start: 0.8146 (mt0) cc_final: 0.7918 (tt0) REVERT: C 206 ASP cc_start: 0.8379 (t0) cc_final: 0.7995 (t70) REVERT: C 216 GLN cc_start: 0.8590 (tp40) cc_final: 0.8211 (tp-100) REVERT: C 222 TYR cc_start: 0.9040 (t80) cc_final: 0.8234 (t80) REVERT: C 224 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8649 (mm110) REVERT: C 280 LYS cc_start: 0.8567 (tttt) cc_final: 0.7871 (tptt) REVERT: D 279 TYR cc_start: 0.8763 (p90) cc_final: 0.8143 (p90) REVERT: D 293 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7806 (tptp) REVERT: E 183 MET cc_start: 0.8669 (ttm) cc_final: 0.7848 (mtp) REVERT: E 229 MET cc_start: 0.8954 (mtt) cc_final: 0.8652 (mtt) REVERT: B 110 ASP cc_start: 0.8917 (t0) cc_final: 0.8627 (t0) REVERT: B 229 MET cc_start: 0.8153 (mtt) cc_final: 0.7838 (mpp) outliers start: 60 outliers final: 52 residues processed: 347 average time/residue: 0.0894 time to fit residues: 45.8293 Evaluate side-chains 365 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain L residue 84 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 110 ASP Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 178 SER 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 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 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 183 MET 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 E residue 92 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 210 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** E 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 = 0.3314 r_free = 0.3314 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.108103 restraints weight = 17198.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110641 restraints weight = 7611.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.112151 restraints weight = 4219.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.113024 restraints weight = 2807.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.113588 restraints weight = 2206.500| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3832 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= 0.171 Angle : 0.708 9.941 15045 Z= 0.351 Chirality : 0.048 0.268 1592 Planarity : 0.005 0.063 1932 Dihedral : 8.195 57.597 1561 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.80 % Rotamer: Outliers : 5.46 % Allowed : 21.82 % Favored : 72.72 % 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: -2.10 (0.22), residues: 1305 helix: -2.03 (0.51), residues: 97 sheet: -0.16 (0.28), residues: 325 loop : -1.93 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.020 0.002 TYR C 201 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 covalent geometry : bond 0.00421 (11072) covalent geometry : angle 0.70829 (15041) SS BOND : bond 0.00141 ( 2) SS BOND : angle 1.08281 ( 4) hydrogen bonds : bond 0.03008 ( 202) hydrogen bonds : angle 5.06129 ( 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 383 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 319 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5486 (pp) REVERT: H 32 TYR cc_start: 0.6222 (p90) cc_final: 0.6009 (p90) REVERT: H 34 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6975 (ttp) REVERT: A 205 TYR cc_start: 0.8742 (t80) cc_final: 0.8483 (t80) REVERT: A 224 GLN cc_start: 0.8922 (mm110) cc_final: 0.8545 (mm-40) REVERT: A 235 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (pt) REVERT: A 280 LYS cc_start: 0.6935 (tptt) cc_final: 0.6391 (tptt) REVERT: C 189 GLN cc_start: 0.8836 (mt0) cc_final: 0.8588 (tt0) REVERT: C 206 ASP cc_start: 0.8470 (t0) cc_final: 0.8008 (t70) REVERT: C 216 GLN cc_start: 0.8605 (tp40) cc_final: 0.8175 (tp-100) REVERT: C 222 TYR cc_start: 0.9059 (t80) cc_final: 0.8258 (t80) REVERT: C 224 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8665 (mm110) REVERT: C 264 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8605 (mtp85) REVERT: C 280 LYS cc_start: 0.8534 (tttt) cc_final: 0.7856 (tptt) REVERT: D 279 TYR cc_start: 0.8735 (p90) cc_final: 0.8219 (p90) REVERT: D 293 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7845 (tptp) REVERT: E 183 MET cc_start: 0.8670 (ttm) cc_final: 0.7865 (mtp) REVERT: E 229 MET cc_start: 0.8970 (mtt) cc_final: 0.8672 (mtt) REVERT: B 229 MET cc_start: 0.8165 (mtt) cc_final: 0.7877 (mpp) outliers start: 64 outliers final: 55 residues processed: 348 average time/residue: 0.0901 time to fit residues: 46.3655 Evaluate side-chains 374 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 316 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 34 MET 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 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 190 VAL Chi-restraints excluded: chain C residue 195 MET 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 95 MET Chi-restraints excluded: chain D residue 146 LEU 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 248 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 210 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN D 282 ASN E 189 GLN ** E 278 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.124571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.106264 restraints weight = 17655.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.108833 restraints weight = 7614.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110358 restraints weight = 4161.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111292 restraints weight = 2743.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.111704 restraints weight = 2116.581| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11074 Z= 0.285 Angle : 0.781 10.597 15045 Z= 0.392 Chirality : 0.051 0.259 1592 Planarity : 0.006 0.062 1932 Dihedral : 8.650 59.359 1561 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.27 % Favored : 89.50 % Rotamer: Outliers : 6.22 % Allowed : 21.57 % Favored : 72.21 % 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: -2.08 (0.23), residues: 1305 helix: -1.99 (0.53), residues: 97 sheet: -0.23 (0.29), residues: 331 loop : -1.89 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.021 0.002 TYR C 201 PHE 0.011 0.002 PHE A 135 TRP 0.021 0.002 TRP L 56 HIS 0.005 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00699 (11072) covalent geometry : angle 0.78105 (15041) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.28745 ( 4) hydrogen bonds : bond 0.03709 ( 202) hydrogen bonds : angle 5.29304 ( 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 393 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5374 (pp) REVERT: L 95 GLN cc_start: 0.5745 (OUTLIER) cc_final: 0.5398 (pt0) REVERT: H 34 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7156 (ttp) REVERT: H 57 ASP cc_start: 0.8918 (p0) cc_final: 0.7996 (p0) REVERT: A 205 TYR cc_start: 0.8870 (t80) cc_final: 0.8622 (t80) REVERT: A 235 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (pt) REVERT: A 280 LYS cc_start: 0.6785 (tptt) cc_final: 0.6181 (tptt) REVERT: C 122 LYS cc_start: 0.8944 (mtpt) cc_final: 0.7934 (mmtt) REVERT: C 206 ASP cc_start: 0.8447 (t0) cc_final: 0.8003 (t70) REVERT: C 213 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 216 GLN cc_start: 0.8676 (tp40) cc_final: 0.8206 (tp-100) REVERT: C 222 TYR cc_start: 0.9081 (t80) cc_final: 0.8702 (t80) REVERT: C 224 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9066 (mm110) REVERT: C 242 LYS cc_start: 0.8680 (tttp) cc_final: 0.8476 (tmtt) REVERT: C 280 LYS cc_start: 0.8731 (tttt) cc_final: 0.7867 (tptt) REVERT: D 279 TYR cc_start: 0.8863 (p90) cc_final: 0.8172 (p90) REVERT: D 293 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7767 (tptp) REVERT: E 183 MET cc_start: 0.8739 (ttm) cc_final: 0.7965 (mtp) REVERT: E 229 MET cc_start: 0.9089 (mtt) cc_final: 0.8795 (mtt) REVERT: B 141 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8687 (mtpt) REVERT: B 229 MET cc_start: 0.8459 (mtt) cc_final: 0.7905 (mpp) outliers start: 73 outliers final: 62 residues processed: 352 average time/residue: 0.0841 time to fit residues: 43.8108 Evaluate side-chains 373 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 34 MET 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 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 238 VAL 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 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 129 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 175 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 238 VAL 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 122 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 210 THR 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 95 MET Chi-restraints excluded: chain B residue 191 SER 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: 3.9990 chunk 117 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 278 ASN D 214 HIS D 269 GLN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 82 ASN B 189 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108262 restraints weight = 17283.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110785 restraints weight = 7683.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.112319 restraints weight = 4272.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.113211 restraints weight = 2839.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.113797 restraints weight = 2219.123| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11074 Z= 0.157 Angle : 0.712 10.704 15045 Z= 0.354 Chirality : 0.048 0.242 1592 Planarity : 0.005 0.061 1932 Dihedral : 8.379 58.364 1561 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.74 % Favored : 91.11 % Rotamer: Outliers : 4.60 % Allowed : 23.10 % Favored : 72.29 % 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: -1.91 (0.23), residues: 1305 helix: -1.95 (0.51), residues: 97 sheet: -0.11 (0.29), residues: 325 loop : -1.75 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.039 0.002 TYR L 100 PHE 0.013 0.001 PHE B 233 TRP 0.026 0.001 TRP L 56 HIS 0.002 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00387 (11072) covalent geometry : angle 0.71159 (15041) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.08867 ( 4) hydrogen bonds : bond 0.02993 ( 202) hydrogen bonds : angle 5.04226 ( 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 378 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 0.434 Fit side-chains REVERT: L 29 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5556 (pp) REVERT: L 51 GLN cc_start: 0.5784 (mp10) cc_final: 0.5203 (mp10) REVERT: H 35 LYS cc_start: 0.8550 (mppt) cc_final: 0.8126 (mptt) REVERT: A 76 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 205 TYR cc_start: 0.8803 (t80) cc_final: 0.8585 (t80) REVERT: A 235 ILE cc_start: 0.9364 (pt) cc_final: 0.9118 (pt) REVERT: A 280 LYS cc_start: 0.6800 (tptt) cc_final: 0.6169 (tptt) REVERT: C 189 GLN cc_start: 0.9007 (mt0) cc_final: 0.8764 (tt0) REVERT: C 206 ASP cc_start: 0.8395 (t0) cc_final: 0.7946 (t70) REVERT: C 213 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8138 (mm-30) REVERT: C 216 GLN cc_start: 0.8601 (tp40) cc_final: 0.8131 (tp-100) REVERT: C 222 TYR cc_start: 0.9126 (t80) cc_final: 0.8709 (t80) REVERT: C 280 LYS cc_start: 0.8619 (tttt) cc_final: 0.7869 (tptt) REVERT: D 279 TYR cc_start: 0.8549 (p90) cc_final: 0.8071 (p90) REVERT: D 293 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7849 (tptp) REVERT: E 183 MET cc_start: 0.8568 (ttm) cc_final: 0.7775 (mtp) REVERT: E 229 MET cc_start: 0.8951 (mtt) cc_final: 0.8669 (mtt) REVERT: B 229 MET cc_start: 0.8178 (mtt) cc_final: 0.7786 (mpp) outliers start: 54 outliers final: 44 residues processed: 349 average time/residue: 0.0860 time to fit residues: 44.6884 Evaluate side-chains 362 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 317 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 64 VAL 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 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 238 VAL 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 190 VAL 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 C residue 295 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 210 THR 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 95 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 278 ASN D 269 GLN E 189 GLN ** E 278 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112884 restraints weight = 17317.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.115493 restraints weight = 7400.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117045 restraints weight = 4029.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117928 restraints weight = 2661.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118495 restraints weight = 2079.837| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11074 Z= 0.127 Angle : 0.697 10.417 15045 Z= 0.344 Chirality : 0.047 0.223 1592 Planarity : 0.005 0.061 1932 Dihedral : 7.900 59.253 1561 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 3.32 % Allowed : 25.15 % Favored : 71.53 % 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: -1.75 (0.23), residues: 1305 helix: -1.74 (0.53), residues: 97 sheet: 0.02 (0.29), residues: 323 loop : -1.65 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 120 TYR 0.036 0.001 TYR L 100 PHE 0.013 0.001 PHE B 233 TRP 0.026 0.001 TRP L 56 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00313 (11072) covalent geometry : angle 0.69719 (15041) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.96558 ( 4) hydrogen bonds : bond 0.02805 ( 202) hydrogen bonds : angle 4.85978 ( 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 365 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.412 Fit side-chains REVERT: L 29 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5350 (pp) REVERT: L 109 LYS cc_start: 0.6440 (tptp) cc_final: 0.6093 (tptp) REVERT: H 35 LYS cc_start: 0.8469 (mppt) cc_final: 0.7985 (mptt) REVERT: H 57 ASP cc_start: 0.8836 (p0) cc_final: 0.7757 (p0) REVERT: H 96 CYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8000 (p) REVERT: A 76 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 235 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9073 (pt) REVERT: A 243 SER cc_start: 0.9359 (p) cc_final: 0.9120 (t) REVERT: A 280 LYS cc_start: 0.6817 (tptt) cc_final: 0.6243 (tptt) REVERT: C 189 GLN cc_start: 0.8824 (mt0) cc_final: 0.8594 (tt0) REVERT: C 206 ASP cc_start: 0.8309 (t0) cc_final: 0.7843 (t70) REVERT: C 213 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8222 (mm-30) REVERT: C 222 TYR cc_start: 0.9023 (t80) cc_final: 0.8646 (t80) REVERT: C 264 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8587 (mtp85) REVERT: C 280 LYS cc_start: 0.8572 (tttt) cc_final: 0.7761 (tptt) REVERT: D 269 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8830 (mm110) REVERT: D 279 TYR cc_start: 0.8483 (p90) cc_final: 0.8064 (p90) REVERT: D 293 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7796 (tptp) REVERT: E 183 MET cc_start: 0.8495 (ttm) cc_final: 0.7826 (mtp) REVERT: E 229 MET cc_start: 0.8982 (mtt) cc_final: 0.8675 (mtt) REVERT: B 110 ASP cc_start: 0.8867 (t0) cc_final: 0.8596 (t0) REVERT: B 189 GLN cc_start: 0.8898 (tt0) cc_final: 0.8680 (tt0) REVERT: B 229 MET cc_start: 0.8205 (mtt) cc_final: 0.7814 (mpp) outliers start: 39 outliers final: 32 residues processed: 347 average time/residue: 0.0820 time to fit residues: 42.1601 Evaluate side-chains 355 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 64 VAL 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 185 ASP 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 190 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 234 SER 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 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN A 224 GLN ** E 278 ASN ** 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 = 0.3365 r_free = 0.3365 target = 0.130692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.112164 restraints weight = 17433.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114795 restraints weight = 7447.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116351 restraints weight = 4035.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117315 restraints weight = 2648.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117822 restraints weight = 2037.548| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 0.058 11074 Z= 0.173 Angle : 0.715 9.658 15045 Z= 0.353 Chirality : 0.048 0.222 1592 Planarity : 0.005 0.062 1932 Dihedral : 7.908 59.570 1561 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.12 % Favored : 90.73 % Rotamer: Outliers : 3.75 % Allowed : 25.06 % Favored : 71.18 % 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: -1.71 (0.23), residues: 1305 helix: -1.64 (0.54), residues: 97 sheet: 0.02 (0.29), residues: 325 loop : -1.63 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.037 0.002 TYR L 100 PHE 0.011 0.001 PHE B 233 TRP 0.029 0.001 TRP L 56 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00429 (11072) covalent geometry : angle 0.71476 (15041) SS BOND : bond 0.00049 ( 2) SS BOND : angle 1.00859 ( 4) hydrogen bonds : bond 0.02987 ( 202) hydrogen bonds : angle 4.91581 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.74 seconds wall clock time: 32 minutes 44.92 seconds (1964.92 seconds total)