Starting phenix.real_space_refine on Mon Jul 28 18:28:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_0897.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_0897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_0897.map" model { file = "/net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_0897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lht_0897/07_2025/6lht_0897.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.47, per 1000 atoms: 0.60 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.19 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: 2.61 Time building geometry restraints manager: 2.80 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP L 102 HIS 0.004 0.001 HIS B 245 PHE 0.032 0.002 PHE H 107 TYR 0.040 0.002 TYR L 55 ARG 0.003 0.001 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.27681 ( 202) hydrogen bonds : angle 10.58894 ( 765) SS BOND : bond 0.01375 ( 2) SS BOND : angle 2.82795 ( 4) covalent geometry : bond 0.00795 (11072) covalent geometry : angle 1.15421 (15041) *********************** 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 : 1.261 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: 0.2098 time to fit residues: 117.1308 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 : 1.192 ------------------------------------------------------------------------------- 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 110 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 A 73 HIS A 82 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 76 GLN E 82 ASN E 224 GLN B 76 GLN B 82 ASN B 245 HIS B 257 HIS B 276 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.134805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.116166 restraints weight = 17074.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.118937 restraints weight = 7347.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120602 restraints weight = 4002.123| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11074 Z= 0.164 Angle : 0.735 11.386 15045 Z= 0.379 Chirality : 0.048 0.271 1592 Planarity : 0.006 0.065 1932 Dihedral : 10.159 59.870 1575 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.43 % Favored : 92.11 % Rotamer: Outliers : 3.58 % Allowed : 16.54 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.20), residues: 1305 helix: -4.16 (0.24), residues: 117 sheet: -0.95 (0.26), residues: 357 loop : -2.87 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 261 HIS 0.002 0.001 HIS A 72 PHE 0.009 0.001 PHE L 104 TYR 0.034 0.002 TYR H 80 ARG 0.006 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 202) hydrogen bonds : angle 5.87473 ( 765) SS BOND : bond 0.00410 ( 2) SS BOND : angle 0.99111 ( 4) covalent geometry : bond 0.00370 (11072) covalent geometry : angle 0.73446 (15041) *********************** 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 382 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 340 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 87 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8074 (tp30) REVERT: H 32 TYR cc_start: 0.5935 (p90) cc_final: 0.5605 (p90) REVERT: H 33 TYR cc_start: 0.7644 (m-10) cc_final: 0.7241 (m-10) REVERT: H 57 ASP cc_start: 0.8525 (p0) cc_final: 0.8146 (p0) REVERT: H 59 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: A 167 ASP cc_start: 0.8077 (p0) cc_final: 0.7798 (p0) REVERT: A 272 LEU cc_start: 0.9275 (mt) cc_final: 0.9053 (mt) REVERT: A 280 LYS cc_start: 0.6344 (tptt) cc_final: 0.5713 (tptt) REVERT: C 122 LYS cc_start: 0.8839 (mtpt) cc_final: 0.7772 (mmtt) REVERT: C 191 SER cc_start: 0.8598 (m) cc_final: 0.8298 (t) REVERT: C 222 TYR cc_start: 0.8890 (t80) cc_final: 0.8566 (t80) REVERT: C 242 LYS cc_start: 0.8498 (tttp) cc_final: 0.8268 (tttt) REVERT: C 280 LYS cc_start: 0.8431 (tttt) cc_final: 0.7666 (tptt) REVERT: D 122 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8810 (ttpt) REVERT: D 124 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8036 (mt-10) REVERT: D 167 ASP cc_start: 0.8242 (p0) cc_final: 0.8008 (p0) REVERT: D 183 MET cc_start: 0.8471 (mtp) cc_final: 0.8170 (mtm) REVERT: D 195 MET cc_start: 0.8691 (ptm) cc_final: 0.8459 (ptp) REVERT: D 279 TYR cc_start: 0.8771 (p90) cc_final: 0.8163 (p90) REVERT: D 293 LYS cc_start: 0.8511 (mttp) cc_final: 0.8032 (tptp) REVERT: E 106 TYR cc_start: 0.9059 (p90) cc_final: 0.8803 (p90) REVERT: E 124 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8275 (mt-10) REVERT: E 153 TYR cc_start: 0.9420 (m-80) cc_final: 0.9164 (m-80) REVERT: E 222 TYR cc_start: 0.8793 (t80) cc_final: 0.8472 (t80) REVERT: E 229 MET cc_start: 0.9066 (mtt) cc_final: 0.8738 (mpp) REVERT: B 110 ASP cc_start: 0.8876 (t0) cc_final: 0.8620 (t0) REVERT: B 229 MET cc_start: 0.8367 (mtt) cc_final: 0.7858 (mpp) REVERT: B 230 MET cc_start: 0.7600 (mmm) cc_final: 0.7394 (mmm) REVERT: B 280 LYS cc_start: 0.8246 (tttt) cc_final: 0.7788 (tptt) REVERT: B 290 SER cc_start: 0.8009 (t) cc_final: 0.7610 (t) outliers start: 42 outliers final: 27 residues processed: 361 average time/residue: 0.2228 time to fit residues: 116.8359 Evaluate side-chains 339 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 232 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 295 THR Chi-restraints excluded: chain D residue 164 THR 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 122 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 288 SER 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 275 THR Chi-restraints excluded: chain B residue 276 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 4 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 0.0060 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 overall best weight: 3.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN H 61 ASN H 62 GLN A 73 HIS A 176 ASN A 278 ASN C 216 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN B 76 GLN B 82 ASN B 176 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113587 restraints weight = 17357.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.116161 restraints weight = 7668.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117679 restraints weight = 4254.874| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2502 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= 0.161 Angle : 0.692 10.559 15045 Z= 0.354 Chirality : 0.047 0.253 1592 Planarity : 0.005 0.063 1932 Dihedral : 8.955 59.782 1561 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.43 % Favored : 92.18 % Rotamer: Outliers : 4.09 % Allowed : 18.58 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.21), residues: 1305 helix: -3.20 (0.39), residues: 97 sheet: -0.63 (0.26), residues: 365 loop : -2.57 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 102 HIS 0.002 0.001 HIS E 257 PHE 0.012 0.001 PHE L 104 TYR 0.029 0.002 TYR H 80 ARG 0.005 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 202) hydrogen bonds : angle 5.42652 ( 765) SS BOND : bond 0.00395 ( 2) SS BOND : angle 1.08194 ( 4) covalent geometry : bond 0.00385 (11072) covalent geometry : angle 0.69185 (15041) *********************** 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 371 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 55 TYR cc_start: 0.5800 (m-80) cc_final: 0.5238 (m-80) REVERT: H 32 TYR cc_start: 0.6053 (p90) cc_final: 0.5733 (p90) REVERT: H 33 TYR cc_start: 0.7692 (m-10) cc_final: 0.7380 (m-10) REVERT: H 39 GLN cc_start: 0.7786 (pp30) cc_final: 0.7040 (pp30) REVERT: H 57 ASP cc_start: 0.8390 (p0) cc_final: 0.7874 (p0) REVERT: H 83 LEU cc_start: 0.6819 (pt) cc_final: 0.6549 (pt) REVERT: A 167 ASP cc_start: 0.8002 (p0) cc_final: 0.7571 (p0) REVERT: A 280 LYS cc_start: 0.6524 (tptt) cc_final: 0.5794 (tptt) REVERT: C 110 ASP cc_start: 0.8941 (t0) cc_final: 0.8644 (t0) REVERT: C 122 LYS cc_start: 0.8832 (mtpt) cc_final: 0.7855 (mmtt) REVERT: C 129 MET cc_start: 0.8480 (mtp) cc_final: 0.8126 (mtm) REVERT: C 191 SER cc_start: 0.8727 (m) cc_final: 0.8392 (t) REVERT: C 206 ASP cc_start: 0.8231 (t0) cc_final: 0.7786 (t70) REVERT: C 222 TYR cc_start: 0.8884 (t80) cc_final: 0.8606 (t80) REVERT: C 280 LYS cc_start: 0.8445 (tttt) cc_final: 0.7706 (tptt) REVERT: D 122 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8874 (ttpt) REVERT: D 167 ASP cc_start: 0.8107 (p0) cc_final: 0.7852 (p0) REVERT: D 279 TYR cc_start: 0.8720 (p90) cc_final: 0.8163 (p90) REVERT: E 222 TYR cc_start: 0.8766 (t80) cc_final: 0.8498 (t80) REVERT: E 229 MET cc_start: 0.8949 (mtt) cc_final: 0.8685 (mpp) REVERT: B 280 LYS cc_start: 0.8286 (tttt) cc_final: 0.7914 (tptt) outliers start: 48 outliers final: 36 residues processed: 345 average time/residue: 0.2607 time to fit residues: 131.9313 Evaluate side-chains 345 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 294 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 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 211 PHE 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 18 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** B 276 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 = 0.3392 r_free = 0.3392 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.114145 restraints weight = 17203.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116683 restraints weight = 7604.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.118224 restraints weight = 4204.726| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11074 Z= 0.121 Angle : 0.665 10.700 15045 Z= 0.334 Chirality : 0.046 0.227 1592 Planarity : 0.005 0.061 1932 Dihedral : 8.105 58.545 1561 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 3.58 % Allowed : 20.20 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.22), residues: 1305 helix: -2.67 (0.44), residues: 97 sheet: -0.22 (0.28), residues: 340 loop : -2.27 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 56 HIS 0.002 0.000 HIS B 73 PHE 0.013 0.001 PHE L 104 TYR 0.026 0.001 TYR L 100 ARG 0.004 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02785 ( 202) hydrogen bonds : angle 5.07983 ( 765) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.85782 ( 4) covalent geometry : bond 0.00287 (11072) covalent geometry : angle 0.66459 (15041) *********************** 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 372 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5275 (pp) REVERT: H 32 TYR cc_start: 0.5914 (p90) cc_final: 0.5659 (p90) REVERT: H 33 TYR cc_start: 0.7589 (m-10) cc_final: 0.7360 (m-10) REVERT: H 34 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6528 (ttp) REVERT: H 39 GLN cc_start: 0.7713 (pp30) cc_final: 0.6901 (pp30) REVERT: H 46 GLU cc_start: 0.6893 (pm20) cc_final: 0.6637 (pm20) REVERT: H 57 ASP cc_start: 0.8345 (p0) cc_final: 0.7882 (p0) REVERT: H 83 LEU cc_start: 0.6902 (pt) cc_final: 0.6649 (pt) REVERT: A 154 MET cc_start: 0.8816 (ttt) cc_final: 0.8604 (ttt) REVERT: A 167 ASP cc_start: 0.7924 (p0) cc_final: 0.7527 (p0) REVERT: A 280 LYS cc_start: 0.6583 (tptt) cc_final: 0.6283 (tptt) REVERT: C 110 ASP cc_start: 0.8909 (t0) cc_final: 0.8637 (t0) REVERT: C 129 MET cc_start: 0.8443 (mtp) cc_final: 0.8192 (mtm) REVERT: C 191 SER cc_start: 0.8768 (m) cc_final: 0.8472 (t) REVERT: C 206 ASP cc_start: 0.8316 (t0) cc_final: 0.7857 (t70) REVERT: C 216 GLN cc_start: 0.8544 (tp40) cc_final: 0.8251 (tp-100) REVERT: C 222 TYR cc_start: 0.8907 (t80) cc_final: 0.8555 (t80) REVERT: C 280 LYS cc_start: 0.8297 (tttt) cc_final: 0.7559 (tptt) REVERT: D 108 ASN cc_start: 0.8022 (t0) cc_final: 0.7714 (t0) REVERT: D 167 ASP cc_start: 0.8055 (p0) cc_final: 0.7797 (p0) REVERT: D 230 MET cc_start: 0.8358 (mmp) cc_final: 0.8076 (mmp) REVERT: D 279 TYR cc_start: 0.8546 (p90) cc_final: 0.8191 (p90) REVERT: E 222 TYR cc_start: 0.8671 (t80) cc_final: 0.8425 (t80) REVERT: E 229 MET cc_start: 0.8939 (mtt) cc_final: 0.8661 (mpp) REVERT: B 280 LYS cc_start: 0.8226 (tttt) cc_final: 0.7804 (tptt) outliers start: 42 outliers final: 27 residues processed: 347 average time/residue: 0.2929 time to fit residues: 148.7082 Evaluate side-chains 340 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 311 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL 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 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 219 ASP 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 235 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 8 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 0.0770 chunk 124 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 overall best weight: 4.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.111582 restraints weight = 17282.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.114200 restraints weight = 7480.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115778 restraints weight = 4077.797| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11074 Z= 0.171 Angle : 0.690 10.642 15045 Z= 0.346 Chirality : 0.047 0.240 1592 Planarity : 0.005 0.064 1932 Dihedral : 7.907 59.231 1561 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.89 % Favored : 91.88 % Rotamer: Outliers : 5.54 % Allowed : 19.69 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.22), residues: 1305 helix: -2.29 (0.49), residues: 97 sheet: -0.10 (0.27), residues: 346 loop : -2.15 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 PHE 0.013 0.001 PHE L 104 TYR 0.029 0.002 TYR L 100 ARG 0.004 0.000 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 202) hydrogen bonds : angle 5.05035 ( 765) SS BOND : bond 0.00218 ( 2) SS BOND : angle 1.01339 ( 4) covalent geometry : bond 0.00422 (11072) covalent geometry : angle 0.68994 (15041) *********************** 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 391 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 326 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5030 (pp) REVERT: L 59 THR cc_start: 0.7276 (p) cc_final: 0.7037 (p) REVERT: H 32 TYR cc_start: 0.6043 (p90) cc_final: 0.5766 (p90) REVERT: H 34 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6698 (ttp) REVERT: H 39 GLN cc_start: 0.7801 (pp30) cc_final: 0.6918 (pp30) REVERT: H 46 GLU cc_start: 0.6788 (pm20) cc_final: 0.6570 (pm20) REVERT: H 57 ASP cc_start: 0.8384 (p0) cc_final: 0.7728 (p0) REVERT: A 201 TYR cc_start: 0.9162 (m-80) cc_final: 0.8948 (m-80) REVERT: A 205 TYR cc_start: 0.8625 (t80) cc_final: 0.8421 (t80) REVERT: A 280 LYS cc_start: 0.6760 (tptt) cc_final: 0.6283 (tptt) REVERT: C 129 MET cc_start: 0.8506 (mtp) cc_final: 0.8292 (mtm) REVERT: C 191 SER cc_start: 0.8789 (m) cc_final: 0.8557 (t) REVERT: C 206 ASP cc_start: 0.8436 (t0) cc_final: 0.7951 (t70) REVERT: C 216 GLN cc_start: 0.8615 (tp40) cc_final: 0.8272 (tp-100) REVERT: C 222 TYR cc_start: 0.8968 (t80) cc_final: 0.8712 (t80) REVERT: C 280 LYS cc_start: 0.8400 (tttt) cc_final: 0.7626 (tptt) REVERT: C 283 ASP cc_start: 0.7896 (t0) cc_final: 0.7580 (t0) REVERT: D 108 ASN cc_start: 0.8188 (t0) cc_final: 0.7879 (t0) REVERT: D 167 ASP cc_start: 0.8260 (p0) cc_final: 0.8025 (p0) REVERT: D 271 TYR cc_start: 0.9448 (m-80) cc_final: 0.9180 (m-80) REVERT: D 279 TYR cc_start: 0.8774 (p90) cc_final: 0.8188 (p90) REVERT: D 293 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7684 (tptp) REVERT: E 222 TYR cc_start: 0.8769 (t80) cc_final: 0.8568 (t80) REVERT: E 229 MET cc_start: 0.9026 (mtt) cc_final: 0.8815 (mtt) REVERT: B 110 ASP cc_start: 0.8907 (t0) cc_final: 0.8567 (t0) REVERT: B 141 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8819 (mtpt) REVERT: B 229 MET cc_start: 0.8362 (mpp) cc_final: 0.7628 (mpp) REVERT: B 280 LYS cc_start: 0.8297 (tttt) cc_final: 0.7850 (tptt) outliers start: 65 outliers final: 54 residues processed: 354 average time/residue: 0.2604 time to fit residues: 135.3528 Evaluate side-chains 362 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR 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 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 185 ASP 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 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 178 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 246 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 105 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.0570 chunk 87 optimal weight: 0.1980 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113421 restraints weight = 17261.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116014 restraints weight = 7363.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117634 restraints weight = 4013.394| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11074 Z= 0.126 Angle : 0.667 10.564 15045 Z= 0.330 Chirality : 0.046 0.242 1592 Planarity : 0.005 0.059 1932 Dihedral : 7.669 59.595 1561 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.35 % Favored : 91.49 % Rotamer: Outliers : 5.03 % Allowed : 21.57 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.22), residues: 1305 helix: -2.10 (0.50), residues: 97 sheet: -0.01 (0.28), residues: 331 loop : -1.99 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 56 HIS 0.003 0.000 HIS B 214 PHE 0.010 0.001 PHE L 104 TYR 0.025 0.001 TYR L 100 ARG 0.005 0.000 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 202) hydrogen bonds : angle 4.85409 ( 765) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.81715 ( 4) covalent geometry : bond 0.00310 (11072) covalent geometry : angle 0.66690 (15041) *********************** 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 385 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 1.227 Fit side-chains REVERT: L 29 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.4985 (pp) REVERT: L 59 THR cc_start: 0.6976 (p) cc_final: 0.6706 (p) REVERT: H 34 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6733 (ttp) REVERT: H 39 GLN cc_start: 0.7844 (pp30) cc_final: 0.6920 (pp30) REVERT: H 46 GLU cc_start: 0.6770 (pm20) cc_final: 0.6557 (pm20) REVERT: H 59 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: A 205 TYR cc_start: 0.8610 (t80) cc_final: 0.8370 (t80) REVERT: A 280 LYS cc_start: 0.6689 (tptt) cc_final: 0.6210 (tptt) REVERT: C 189 GLN cc_start: 0.9148 (tt0) cc_final: 0.8801 (tt0) REVERT: C 206 ASP cc_start: 0.8421 (t0) cc_final: 0.7974 (t70) REVERT: C 216 GLN cc_start: 0.8649 (tp40) cc_final: 0.8306 (tp-100) REVERT: C 222 TYR cc_start: 0.8946 (t80) cc_final: 0.8425 (t80) REVERT: C 224 GLN cc_start: 0.8979 (mm110) cc_final: 0.8777 (mm-40) REVERT: C 280 LYS cc_start: 0.8442 (tttt) cc_final: 0.7630 (tptt) REVERT: C 283 ASP cc_start: 0.8037 (t0) cc_final: 0.7722 (t0) REVERT: D 108 ASN cc_start: 0.8111 (t0) cc_final: 0.7840 (t0) REVERT: D 279 TYR cc_start: 0.8712 (p90) cc_final: 0.8236 (p90) REVERT: D 293 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7823 (tptp) REVERT: E 111 ILE cc_start: 0.9059 (mt) cc_final: 0.8815 (mt) REVERT: E 183 MET cc_start: 0.8734 (ttm) cc_final: 0.7784 (mtp) REVERT: B 110 ASP cc_start: 0.8871 (t0) cc_final: 0.8542 (t0) REVERT: B 280 LYS cc_start: 0.8218 (tttt) cc_final: 0.7798 (tptt) outliers start: 59 outliers final: 45 residues processed: 353 average time/residue: 0.2235 time to fit residues: 116.0567 Evaluate side-chains 362 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 ASP 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 146 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** 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 = 0.3345 r_free = 0.3345 target = 0.128881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110362 restraints weight = 17579.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.112888 restraints weight = 7772.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114399 restraints weight = 4299.174| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11074 Z= 0.203 Angle : 0.714 10.660 15045 Z= 0.357 Chirality : 0.048 0.281 1592 Planarity : 0.005 0.059 1932 Dihedral : 7.816 58.897 1561 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.03 % Rotamer: Outliers : 5.46 % Allowed : 21.40 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.23), residues: 1305 helix: -1.89 (0.52), residues: 97 sheet: -0.10 (0.28), residues: 331 loop : -1.88 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 56 HIS 0.004 0.001 HIS E 257 PHE 0.009 0.001 PHE L 104 TYR 0.031 0.002 TYR L 100 ARG 0.004 0.001 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 202) hydrogen bonds : angle 4.99635 ( 765) SS BOND : bond 0.00187 ( 2) SS BOND : angle 1.07804 ( 4) covalent geometry : bond 0.00502 (11072) covalent geometry : angle 0.71372 (15041) *********************** 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 381 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 317 time to evaluate : 1.177 Fit side-chains REVERT: L 29 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5264 (pp) REVERT: L 59 THR cc_start: 0.7212 (p) cc_final: 0.7010 (p) REVERT: H 46 GLU cc_start: 0.7030 (pm20) cc_final: 0.6772 (pm20) REVERT: H 57 ASP cc_start: 0.8724 (p0) cc_final: 0.7690 (p0) REVERT: A 280 LYS cc_start: 0.6839 (tptt) cc_final: 0.6289 (tptt) REVERT: C 206 ASP cc_start: 0.8392 (t0) cc_final: 0.7963 (t70) REVERT: C 216 GLN cc_start: 0.8608 (tp40) cc_final: 0.8308 (tp-100) REVERT: C 222 TYR cc_start: 0.9044 (t80) cc_final: 0.8310 (t80) REVERT: C 224 GLN cc_start: 0.9048 (mm110) cc_final: 0.8729 (mm110) REVERT: C 280 LYS cc_start: 0.8517 (tttt) cc_final: 0.7744 (tptt) REVERT: C 283 ASP cc_start: 0.8071 (t0) cc_final: 0.7826 (t0) REVERT: D 108 ASN cc_start: 0.8151 (t0) cc_final: 0.7853 (t0) REVERT: D 279 TYR cc_start: 0.8788 (p90) cc_final: 0.8244 (p90) REVERT: D 293 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7891 (tptp) REVERT: E 111 ILE cc_start: 0.9178 (mt) cc_final: 0.8927 (mt) REVERT: E 183 MET cc_start: 0.8776 (ttm) cc_final: 0.7902 (mtp) REVERT: B 110 ASP cc_start: 0.8949 (t0) cc_final: 0.8663 (t0) outliers start: 64 outliers final: 54 residues processed: 348 average time/residue: 0.1950 time to fit residues: 98.5196 Evaluate side-chains 364 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 33 ASN Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 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 129 MET 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 D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 178 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 246 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 Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN L 48 GLN C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 218 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.130096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111625 restraints weight = 17336.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114125 restraints weight = 7668.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.115608 restraints weight = 4239.450| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11074 Z= 0.159 Angle : 0.695 10.291 15045 Z= 0.343 Chirality : 0.047 0.214 1592 Planarity : 0.005 0.058 1932 Dihedral : 7.762 58.086 1561 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 4.60 % Allowed : 22.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1305 helix: -1.88 (0.52), residues: 97 sheet: -0.10 (0.28), residues: 331 loop : -1.80 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 56 HIS 0.002 0.001 HIS E 257 PHE 0.009 0.001 PHE A 233 TYR 0.027 0.002 TYR L 100 ARG 0.003 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 202) hydrogen bonds : angle 4.91765 ( 765) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.97244 ( 4) covalent geometry : bond 0.00392 (11072) covalent geometry : angle 0.69498 (15041) *********************** 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 372 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 1.298 Fit side-chains REVERT: L 29 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5168 (pp) REVERT: L 95 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5790 (pt0) REVERT: H 46 GLU cc_start: 0.6994 (pm20) cc_final: 0.6743 (pm20) REVERT: H 57 ASP cc_start: 0.8648 (p0) cc_final: 0.7522 (p0) REVERT: A 280 LYS cc_start: 0.6789 (tptt) cc_final: 0.6239 (tptt) REVERT: C 206 ASP cc_start: 0.8395 (t0) cc_final: 0.7961 (t70) REVERT: C 216 GLN cc_start: 0.8644 (tp40) cc_final: 0.8323 (tp-100) REVERT: C 222 TYR cc_start: 0.9048 (t80) cc_final: 0.8296 (t80) REVERT: C 224 GLN cc_start: 0.9077 (mm110) cc_final: 0.8712 (mm110) REVERT: C 280 LYS cc_start: 0.8522 (tttt) cc_final: 0.7735 (tptt) REVERT: D 108 ASN cc_start: 0.8133 (t0) cc_final: 0.7862 (t0) REVERT: D 279 TYR cc_start: 0.8701 (p90) cc_final: 0.8186 (p90) REVERT: D 293 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7900 (tptp) REVERT: E 183 MET cc_start: 0.8715 (ttm) cc_final: 0.7817 (mtp) REVERT: B 110 ASP cc_start: 0.8923 (t0) cc_final: 0.8631 (t0) outliers start: 54 outliers final: 45 residues processed: 345 average time/residue: 0.2136 time to fit residues: 106.7054 Evaluate side-chains 354 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 33 ASN Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 95 GLN 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 185 ASP 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 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 284 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 178 SER 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 246 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 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 0.0070 chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 60 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN H 5 GLN C 82 ASN C 278 ASN D 269 GLN E 189 GLN B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114318 restraints weight = 17214.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.116856 restraints weight = 7605.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.118352 restraints weight = 4205.749| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11074 Z= 0.114 Angle : 0.675 10.071 15045 Z= 0.332 Chirality : 0.046 0.209 1592 Planarity : 0.005 0.058 1932 Dihedral : 7.470 58.154 1561 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.28 % Favored : 91.57 % Rotamer: Outliers : 3.50 % Allowed : 24.21 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.23), residues: 1305 helix: -1.82 (0.51), residues: 97 sheet: 0.04 (0.29), residues: 329 loop : -1.71 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 56 HIS 0.002 0.000 HIS B 214 PHE 0.012 0.001 PHE A 233 TYR 0.023 0.001 TYR L 100 ARG 0.007 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02634 ( 202) hydrogen bonds : angle 4.75790 ( 765) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.79605 ( 4) covalent geometry : bond 0.00281 (11072) covalent geometry : angle 0.67504 (15041) *********************** 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 367 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 1.142 Fit side-chains REVERT: L 29 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5122 (pp) REVERT: L 55 TYR cc_start: 0.5462 (m-10) cc_final: 0.5258 (m-10) REVERT: H 46 GLU cc_start: 0.6990 (pm20) cc_final: 0.6734 (pm20) REVERT: H 57 ASP cc_start: 0.8086 (p0) cc_final: 0.6978 (p0) REVERT: H 59 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5978 (m-80) REVERT: A 280 LYS cc_start: 0.6778 (tptt) cc_final: 0.6242 (tptt) REVERT: C 206 ASP cc_start: 0.8389 (t0) cc_final: 0.7926 (t70) REVERT: C 216 GLN cc_start: 0.8577 (tp40) cc_final: 0.8241 (tp-100) REVERT: C 222 TYR cc_start: 0.9060 (t80) cc_final: 0.8529 (t80) REVERT: C 224 GLN cc_start: 0.9066 (mm110) cc_final: 0.8820 (mm-40) REVERT: C 249 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9037 (tt) REVERT: C 280 LYS cc_start: 0.8412 (tttt) cc_final: 0.7725 (tptt) REVERT: D 108 ASN cc_start: 0.8092 (t0) cc_final: 0.7888 (t0) REVERT: D 279 TYR cc_start: 0.8635 (p90) cc_final: 0.8209 (p90) REVERT: D 293 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7983 (tptp) REVERT: E 183 MET cc_start: 0.8679 (ttm) cc_final: 0.7830 (mtp) outliers start: 41 outliers final: 35 residues processed: 345 average time/residue: 0.1986 time to fit residues: 100.0494 Evaluate side-chains 349 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 33 ASN Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain H residue 59 PHE 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 124 GLU 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 258 VAL Chi-restraints excluded: chain C residue 91 SER 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 249 LEU 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 185 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 246 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 Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 20.0000 chunk 122 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 90 optimal weight: 0.0170 chunk 82 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN H 5 GLN C 82 ASN C 278 ASN 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 = 0.3395 r_free = 0.3395 target = 0.133010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113807 restraints weight = 17151.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116401 restraints weight = 7450.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117965 restraints weight = 4093.619| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11074 Z= 0.111 Angle : 0.676 10.213 15045 Z= 0.331 Chirality : 0.046 0.215 1592 Planarity : 0.005 0.056 1932 Dihedral : 7.278 59.456 1561 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.89 % Favored : 91.95 % Rotamer: Outliers : 3.24 % Allowed : 24.47 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1305 helix: -1.76 (0.52), residues: 97 sheet: 0.10 (0.29), residues: 329 loop : -1.64 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 56 HIS 0.002 0.000 HIS B 214 PHE 0.013 0.001 PHE A 233 TYR 0.021 0.001 TYR L 100 ARG 0.007 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 202) hydrogen bonds : angle 4.73271 ( 765) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.70512 ( 4) covalent geometry : bond 0.00271 (11072) covalent geometry : angle 0.67551 (15041) ********************** 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 359 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 1.186 Fit side-chains REVERT: L 29 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4841 (pt) REVERT: L 55 TYR cc_start: 0.5396 (m-10) cc_final: 0.5090 (m-10) REVERT: L 95 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5525 (pt0) REVERT: L 113 LYS cc_start: 0.6038 (mmmm) cc_final: 0.5669 (mmmt) REVERT: H 46 GLU cc_start: 0.6769 (pm20) cc_final: 0.6540 (pm20) REVERT: H 57 ASP cc_start: 0.8142 (p0) cc_final: 0.6967 (p0) REVERT: H 59 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6059 (m-80) REVERT: A 76 GLN cc_start: 0.9106 (tp40) cc_final: 0.8829 (tm-30) REVERT: A 280 LYS cc_start: 0.6645 (tptt) cc_final: 0.6113 (tptt) REVERT: C 95 MET cc_start: 0.7946 (mmm) cc_final: 0.7684 (mtp) REVERT: C 206 ASP cc_start: 0.8426 (t0) cc_final: 0.7936 (t70) REVERT: C 216 GLN cc_start: 0.8617 (tp40) cc_final: 0.8242 (tp-100) REVERT: C 222 TYR cc_start: 0.9026 (t80) cc_final: 0.8489 (t80) REVERT: C 224 GLN cc_start: 0.9070 (mm110) cc_final: 0.8787 (mm-40) REVERT: C 249 LEU cc_start: 0.9306 (tp) cc_final: 0.8981 (tt) REVERT: C 280 LYS cc_start: 0.8438 (tttt) cc_final: 0.7678 (tptt) REVERT: C 293 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7984 (mtpp) REVERT: D 108 ASN cc_start: 0.8082 (t0) cc_final: 0.7796 (t0) REVERT: D 293 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7941 (tptp) REVERT: E 183 MET cc_start: 0.8606 (ttm) cc_final: 0.7821 (mtp) outliers start: 38 outliers final: 34 residues processed: 340 average time/residue: 0.1950 time to fit residues: 97.3814 Evaluate side-chains 344 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 59 PHE 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 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 258 VAL Chi-restraints excluded: chain C residue 91 SER 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 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 185 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 246 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 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN C 82 ASN D 269 GLN B 76 GLN B 82 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112964 restraints weight = 17173.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.115595 restraints weight = 7456.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.117110 restraints weight = 4107.818| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11074 Z= 0.132 Angle : 0.672 9.564 15045 Z= 0.330 Chirality : 0.046 0.204 1592 Planarity : 0.005 0.071 1932 Dihedral : 7.264 59.603 1561 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.51 % Favored : 91.34 % Rotamer: Outliers : 3.50 % Allowed : 24.72 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1305 helix: -1.66 (0.53), residues: 97 sheet: 0.20 (0.29), residues: 325 loop : -1.56 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 56 HIS 0.003 0.000 HIS B 214 PHE 0.010 0.001 PHE A 233 TYR 0.024 0.001 TYR L 100 ARG 0.007 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 202) hydrogen bonds : angle 4.71683 ( 765) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.74643 ( 4) covalent geometry : bond 0.00330 (11072) covalent geometry : angle 0.67210 (15041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4380.54 seconds wall clock time: 81 minutes 13.55 seconds (4873.55 seconds total)