Starting phenix.real_space_refine on Sat Feb 7 08:20:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.map" model { file = "/net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rkr_54018/02_2026/9rkr_54018.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 9792 2.51 5 N 2688 2.21 5 O 2784 1.98 5 H 15648 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30996 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "J" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "K" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "L" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "M" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "N" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "O" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "P" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "Q" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "R" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "S" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Chain: "T" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2583 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 2 Time building chain proxies: 6.76, per 1000 atoms: 0.22 Number of scatterers: 30996 At special positions: 0 Unit cell: (149.33, 146.59, 87.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 O 2784 8.00 N 2688 7.00 C 9792 6.00 H 15648 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 887.6 milliseconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 25 sheets defined 45.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.605A pdb=" N THR I 5 " --> pdb=" O ASN I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 17 Processing helix chain 'I' and resid 25 through 45 Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.734A pdb=" N SER I 139 " --> pdb=" O CYS I 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 136 through 140' Processing helix chain 'I' and resid 141 through 157 removed outlier: 3.769A pdb=" N ILE I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 189 through 199 removed outlier: 3.679A pdb=" N GLU I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP I 194 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG I 196 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG I 198 " --> pdb=" O TRP I 194 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG I 199 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 removed outlier: 3.844A pdb=" N LEU J 6 " --> pdb=" O ASN J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 16 Processing helix chain 'J' and resid 25 through 45 removed outlier: 3.991A pdb=" N LEU J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.994A pdb=" N SER J 139 " --> pdb=" O CYS J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 157 removed outlier: 3.862A pdb=" N ILE J 145 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'J' and resid 189 through 198 removed outlier: 4.007A pdb=" N TRP J 194 " --> pdb=" O GLN J 191 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE J 195 " --> pdb=" O ASP J 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG J 196 " --> pdb=" O GLU J 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 16 removed outlier: 3.659A pdb=" N ILE K 12 " --> pdb=" O PRO K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 45 Processing helix chain 'K' and resid 136 through 140 Processing helix chain 'K' and resid 141 through 158 removed outlier: 3.722A pdb=" N ILE K 145 " --> pdb=" O PRO K 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN K 157 " --> pdb=" O ALA K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 195 through 199 removed outlier: 4.288A pdb=" N ARG K 199 " --> pdb=" O ARG K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 4.167A pdb=" N LEU L 6 " --> pdb=" O ASN L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 16 Processing helix chain 'L' and resid 25 through 45 Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.918A pdb=" N VAL L 140 " --> pdb=" O GLU L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 158 removed outlier: 3.835A pdb=" N ILE L 145 " --> pdb=" O PRO L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.800A pdb=" N SER L 188 " --> pdb=" O GLY L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'M' and resid 2 through 7 removed outlier: 3.564A pdb=" N LEU M 6 " --> pdb=" O ASN M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 17 Processing helix chain 'M' and resid 25 through 45 removed outlier: 3.553A pdb=" N LEU M 29 " --> pdb=" O THR M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 158 removed outlier: 3.614A pdb=" N ILE M 145 " --> pdb=" O PRO M 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'M' and resid 189 through 195 removed outlier: 3.709A pdb=" N GLU M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'N' and resid 2 through 7 removed outlier: 3.890A pdb=" N LEU N 6 " --> pdb=" O ASN N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 16 removed outlier: 3.627A pdb=" N ILE N 12 " --> pdb=" O PRO N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.975A pdb=" N SER N 139 " --> pdb=" O CYS N 136 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 136 through 140' Processing helix chain 'N' and resid 141 through 157 removed outlier: 4.031A pdb=" N ILE N 145 " --> pdb=" O PRO N 141 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 188 Processing helix chain 'N' and resid 189 through 194 Processing helix chain 'N' and resid 195 through 198 Processing helix chain 'O' and resid 8 through 16 removed outlier: 3.614A pdb=" N ILE O 12 " --> pdb=" O PRO O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 136 through 140 Processing helix chain 'O' and resid 141 through 158 removed outlier: 3.737A pdb=" N ILE O 145 " --> pdb=" O PRO O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'O' and resid 189 through 194 Processing helix chain 'O' and resid 194 through 199 removed outlier: 4.147A pdb=" N ARG O 198 " --> pdb=" O TRP O 194 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG O 199 " --> pdb=" O PHE O 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 194 through 199' Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 8 through 16 Processing helix chain 'P' and resid 25 through 45 Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 141 through 157 removed outlier: 3.832A pdb=" N ILE P 145 " --> pdb=" O PRO P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 188 Processing helix chain 'P' and resid 189 through 195 Processing helix chain 'P' and resid 196 through 198 No H-bonds generated for 'chain 'P' and resid 196 through 198' Processing helix chain 'Q' and resid 2 through 7 removed outlier: 3.887A pdb=" N LEU Q 6 " --> pdb=" O ASN Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 17 Processing helix chain 'Q' and resid 25 through 45 Processing helix chain 'Q' and resid 136 through 140 removed outlier: 3.723A pdb=" N SER Q 139 " --> pdb=" O CYS Q 136 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL Q 140 " --> pdb=" O GLU Q 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 136 through 140' Processing helix chain 'Q' and resid 141 through 158 removed outlier: 3.866A pdb=" N ILE Q 145 " --> pdb=" O PRO Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 188 Processing helix chain 'Q' and resid 189 through 195 removed outlier: 3.646A pdb=" N GLU Q 193 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP Q 194 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 198 No H-bonds generated for 'chain 'Q' and resid 196 through 198' Processing helix chain 'R' and resid 2 through 7 removed outlier: 3.945A pdb=" N LEU R 6 " --> pdb=" O ASN R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 17 Processing helix chain 'R' and resid 25 through 45 removed outlier: 3.727A pdb=" N LEU R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 removed outlier: 3.625A pdb=" N SER R 139 " --> pdb=" O CYS R 136 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL R 140 " --> pdb=" O GLU R 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 136 through 140' Processing helix chain 'R' and resid 141 through 157 removed outlier: 3.857A pdb=" N ILE R 145 " --> pdb=" O PRO R 141 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'R' and resid 189 through 195 Processing helix chain 'R' and resid 196 through 198 No H-bonds generated for 'chain 'R' and resid 196 through 198' Processing helix chain 'S' and resid 2 through 7 removed outlier: 4.209A pdb=" N LEU S 6 " --> pdb=" O ASN S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 17 removed outlier: 3.656A pdb=" N ILE S 12 " --> pdb=" O PRO S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 45 Processing helix chain 'S' and resid 136 through 140 Processing helix chain 'S' and resid 141 through 158 removed outlier: 3.739A pdb=" N ILE S 145 " --> pdb=" O PRO S 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN S 157 " --> pdb=" O ALA S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 188 Processing helix chain 'S' and resid 189 through 194 removed outlier: 3.520A pdb=" N TRP S 194 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 199 removed outlier: 4.035A pdb=" N ARG S 198 " --> pdb=" O TRP S 194 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG S 199 " --> pdb=" O PHE S 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 194 through 199' Processing helix chain 'T' and resid 2 through 7 removed outlier: 3.666A pdb=" N LEU T 6 " --> pdb=" O ASN T 2 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 17 Processing helix chain 'T' and resid 25 through 45 removed outlier: 3.794A pdb=" N LEU T 31 " --> pdb=" O THR T 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU T 34 " --> pdb=" O SER T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 140 removed outlier: 3.659A pdb=" N VAL T 140 " --> pdb=" O GLU T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 157 removed outlier: 3.857A pdb=" N ILE T 145 " --> pdb=" O PRO T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 188 Processing helix chain 'T' and resid 189 through 196 removed outlier: 4.015A pdb=" N ARG T 196 " --> pdb=" O ASP T 192 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'I' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'J' and resid 52 through 57 removed outlier: 3.649A pdb=" N VAL J 80 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 90 " --> pdb=" O PHE J 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'K' and resid 54 through 57 removed outlier: 3.533A pdb=" N ILE K 54 " --> pdb=" O TYR K 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'L' and resid 52 through 57 removed outlier: 3.660A pdb=" N LEU L 90 " --> pdb=" O PHE L 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 67 through 68 Processing sheet with id=AA9, first strand: chain 'M' and resid 52 through 57 Processing sheet with id=AB1, first strand: chain 'M' and resid 67 through 68 Processing sheet with id=AB2, first strand: chain 'M' and resid 79 through 81 Processing sheet with id=AB3, first strand: chain 'N' and resid 52 through 58 removed outlier: 4.076A pdb=" N LEU N 126 " --> pdb=" O VAL N 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU N 90 " --> pdb=" O PHE N 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 66 through 68 Processing sheet with id=AB5, first strand: chain 'O' and resid 52 through 57 removed outlier: 3.544A pdb=" N VAL O 80 " --> pdb=" O THR O 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'P' and resid 52 through 56 removed outlier: 3.806A pdb=" N PHE P 81 " --> pdb=" O LEU P 90 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU P 90 " --> pdb=" O PHE P 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'Q' and resid 52 through 57 removed outlier: 3.524A pdb=" N ALA Q 128 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 66 through 68 removed outlier: 3.785A pdb=" N ILE Q 67 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 52 through 58 removed outlier: 4.172A pdb=" N LEU R 126 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 66 through 68 Processing sheet with id=AC4, first strand: chain 'S' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'S' and resid 67 through 68 Processing sheet with id=AC6, first strand: chain 'T' and resid 52 through 56 removed outlier: 3.550A pdb=" N GLU T 56 " --> pdb=" O ALA T 128 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA T 128 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR T 129 " --> pdb=" O VAL T 80 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL T 80 " --> pdb=" O THR T 129 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY T 83 " --> pdb=" O SER T 88 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER T 88 " --> pdb=" O GLY T 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 67 through 68 642 hydrogen bonds defined for protein. 1755 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: 7.69 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15624 1.03 - 1.23: 27 1.23 - 1.42: 6310 1.42 - 1.62: 9191 1.62 - 1.81: 144 Bond restraints: 31296 Sorted by residual: bond pdb=" CG PRO R 96 " pdb=" CD PRO R 96 " ideal model delta sigma weight residual 1.503 1.153 0.350 3.40e-02 8.65e+02 1.06e+02 bond pdb=" N PRO R 96 " pdb=" CD PRO R 96 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.02e+00 bond pdb=" N PRO R 96 " pdb=" CA PRO R 96 " ideal model delta sigma weight residual 1.466 1.494 -0.029 1.21e-02 6.83e+03 5.57e+00 bond pdb=" CB PRO T 73 " pdb=" CG PRO T 73 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.25e+00 bond pdb=" CB PRO Q 89 " pdb=" CG PRO Q 89 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.81e+00 ... (remaining 31291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 56698 4.41 - 8.82: 24 8.82 - 13.23: 0 13.23 - 17.63: 0 17.63 - 22.04: 2 Bond angle restraints: 56724 Sorted by residual: angle pdb=" N PRO R 96 " pdb=" CD PRO R 96 " pdb=" CG PRO R 96 " ideal model delta sigma weight residual 103.20 81.16 22.04 1.50e+00 4.44e-01 2.16e+02 angle pdb=" CA PRO R 96 " pdb=" CB PRO R 96 " pdb=" CG PRO R 96 " ideal model delta sigma weight residual 104.50 85.04 19.46 1.90e+00 2.77e-01 1.05e+02 angle pdb=" N PRO R 96 " pdb=" CA PRO R 96 " pdb=" CB PRO R 96 " ideal model delta sigma weight residual 103.39 97.61 5.78 9.40e-01 1.13e+00 3.78e+01 angle pdb=" N ILE R 163 " pdb=" CA ILE R 163 " pdb=" C ILE R 163 " ideal model delta sigma weight residual 113.71 108.09 5.62 9.50e-01 1.11e+00 3.50e+01 angle pdb=" CA PRO O 96 " pdb=" N PRO O 96 " pdb=" CD PRO O 96 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.46e+01 ... (remaining 56719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13168 17.93 - 35.86: 1052 35.86 - 53.78: 335 53.78 - 71.71: 71 71.71 - 89.64: 38 Dihedral angle restraints: 14664 sinusoidal: 8232 harmonic: 6432 Sorted by residual: dihedral pdb=" CA THR S 49 " pdb=" C THR S 49 " pdb=" N PRO S 50 " pdb=" CA PRO S 50 " ideal model delta harmonic sigma weight residual 180.00 149.90 30.10 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA PHE S 48 " pdb=" C PHE S 48 " pdb=" N THR S 49 " pdb=" CA THR S 49 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU R 162 " pdb=" C GLU R 162 " pdb=" N ILE R 163 " pdb=" CA ILE R 163 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 14661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1563 0.031 - 0.061: 505 0.061 - 0.091: 172 0.091 - 0.122: 159 0.122 - 0.152: 25 Chirality restraints: 2424 Sorted by residual: chirality pdb=" CA VAL K 140 " pdb=" N VAL K 140 " pdb=" C VAL K 140 " pdb=" CB VAL K 140 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE M 74 " pdb=" N ILE M 74 " pdb=" C ILE M 74 " pdb=" CB ILE M 74 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE L 93 " pdb=" N ILE L 93 " pdb=" C ILE L 93 " pdb=" CB ILE L 93 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2421 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE O 95 " -0.074 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO O 96 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 96 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO O 96 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Q 88 " -0.053 5.00e-02 4.00e+02 7.90e-02 9.97e+00 pdb=" N PRO Q 89 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO Q 89 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO Q 89 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL N 72 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO N 73 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 73 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 73 " 0.028 5.00e-02 4.00e+02 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1416 2.18 - 2.79: 60158 2.79 - 3.39: 80183 3.39 - 4.00: 97843 4.00 - 4.60: 152794 Nonbonded interactions: 392394 Sorted by model distance: nonbonded pdb=" O SER N 47 " pdb=" HE ARG N 134 " model vdw 1.578 2.450 nonbonded pdb=" H LEU K 69 " pdb=" O ASN K 99 " model vdw 1.585 2.450 nonbonded pdb=" H LEU O 69 " pdb=" O ASN O 99 " model vdw 1.595 2.450 nonbonded pdb=" OE2 GLU I 4 " pdb="HH22 ARG I 33 " model vdw 1.602 2.450 nonbonded pdb=" OE2 GLU N 56 " pdb=" HH TYR N 130 " model vdw 1.606 2.450 ... (remaining 392389 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: 0.01 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 15.720 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: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 31.440 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.350 15648 Z= 0.157 Angle : 0.642 22.042 21228 Z= 0.372 Chirality : 0.043 0.152 2424 Planarity : 0.005 0.108 2748 Dihedral : 13.749 89.640 5856 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1896 helix: 2.29 (0.21), residues: 636 sheet: -1.18 (0.25), residues: 323 loop : -0.30 (0.23), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 23 TYR 0.008 0.001 TYR P 43 PHE 0.028 0.001 PHE O 95 TRP 0.004 0.001 TRP O 154 HIS 0.008 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00393 (15648) covalent geometry : angle 0.64250 (21228) hydrogen bonds : bond 0.20040 ( 642) hydrogen bonds : angle 7.21171 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7864 (tmm) cc_final: 0.7157 (tmm) REVERT: J 127 MET cc_start: 0.7013 (mpp) cc_final: 0.6724 (mmt) REVERT: K 1 MET cc_start: 0.7311 (tmm) cc_final: 0.6391 (tmm) REVERT: K 14 GLU cc_start: 0.8280 (tp30) cc_final: 0.8019 (tp30) REVERT: K 17 LYS cc_start: 0.4552 (ptpt) cc_final: 0.4311 (tttp) REVERT: M 135 ARG cc_start: 0.7172 (ptp-110) cc_final: 0.5351 (tpt-90) REVERT: N 5 THR cc_start: 0.8527 (m) cc_final: 0.8140 (m) REVERT: N 38 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7426 (tm-30) REVERT: O 1 MET cc_start: 0.7597 (tmm) cc_final: 0.6823 (tmm) REVERT: R 96 PRO cc_start: 0.3938 (Cg_endo) cc_final: 0.3689 (Cg_endo) REVERT: R 157 ASN cc_start: 0.8588 (m-40) cc_final: 0.8316 (t0) REVERT: S 71 GLN cc_start: 0.8172 (mp-120) cc_final: 0.7518 (mp-120) REVERT: T 41 GLU cc_start: 0.8069 (tp30) cc_final: 0.7845 (tp30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2999 time to fit residues: 161.8090 Evaluate side-chains 330 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN I 158 ASN J 2 ASN K 191 GLN O 191 GLN P 158 ASN Q 2 ASN Q 102 HIS ** R 158 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 = 0.4235 r_free = 0.4235 target = 0.192068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154390 restraints weight = 79433.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158679 restraints weight = 31734.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161033 restraints weight = 18561.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162246 restraints weight = 14064.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162856 restraints weight = 12350.808| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15648 Z= 0.203 Angle : 0.620 8.635 21228 Z= 0.331 Chirality : 0.046 0.177 2424 Planarity : 0.006 0.056 2748 Dihedral : 6.723 84.723 2136 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 0.84 % Allowed : 8.87 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1896 helix: 2.30 (0.21), residues: 633 sheet: -1.25 (0.25), residues: 326 loop : -0.40 (0.23), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 199 TYR 0.010 0.001 TYR R 3 PHE 0.014 0.001 PHE O 95 TRP 0.007 0.001 TRP L 154 HIS 0.004 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00462 (15648) covalent geometry : angle 0.62038 (21228) hydrogen bonds : bond 0.05543 ( 642) hydrogen bonds : angle 5.85899 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 343 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7889 (tmm) cc_final: 0.7399 (tmm) REVERT: I 93 ILE cc_start: 0.7024 (mt) cc_final: 0.6821 (mp) REVERT: K 17 LYS cc_start: 0.3465 (ptpt) cc_final: 0.2950 (tttp) REVERT: K 199 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7478 (ttp80) REVERT: M 52 LYS cc_start: 0.7158 (tppt) cc_final: 0.6597 (mmtm) REVERT: M 56 GLU cc_start: 0.6807 (pm20) cc_final: 0.6328 (pm20) REVERT: M 135 ARG cc_start: 0.7238 (ptp-110) cc_final: 0.5263 (tpt-90) REVERT: N 2 ASN cc_start: 0.8210 (t0) cc_final: 0.7876 (t0) outliers start: 14 outliers final: 9 residues processed: 346 average time/residue: 0.3188 time to fit residues: 157.6343 Evaluate side-chains 330 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 321 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 28 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN L 2 ASN N 191 GLN Q 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.190439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152549 restraints weight = 78850.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156941 restraints weight = 30867.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159346 restraints weight = 17793.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160620 restraints weight = 13394.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161051 restraints weight = 11703.173| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15648 Z= 0.206 Angle : 0.608 7.356 21228 Z= 0.322 Chirality : 0.046 0.163 2424 Planarity : 0.006 0.047 2748 Dihedral : 6.842 83.812 2136 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 1.44 % Allowed : 11.45 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1896 helix: 2.13 (0.21), residues: 645 sheet: -1.28 (0.26), residues: 326 loop : -0.68 (0.23), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 23 TYR 0.011 0.001 TYR O 43 PHE 0.014 0.001 PHE M 81 TRP 0.007 0.001 TRP L 154 HIS 0.005 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00471 (15648) covalent geometry : angle 0.60847 (21228) hydrogen bonds : bond 0.05155 ( 642) hydrogen bonds : angle 5.50420 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.8081 (tmm) cc_final: 0.7409 (tmm) REVERT: K 17 LYS cc_start: 0.3737 (ptpt) cc_final: 0.2370 (tttp) REVERT: M 135 ARG cc_start: 0.7196 (ptp-110) cc_final: 0.5425 (tpt-90) REVERT: O 1 MET cc_start: 0.7432 (tmm) cc_final: 0.6098 (tmm) REVERT: S 192 ASP cc_start: 0.7362 (m-30) cc_final: 0.7118 (m-30) outliers start: 24 outliers final: 18 residues processed: 345 average time/residue: 0.3068 time to fit residues: 153.0729 Evaluate side-chains 344 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 326 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN L 2 ASN Q 2 ASN T 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153045 restraints weight = 78602.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157465 restraints weight = 30609.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159894 restraints weight = 17554.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161173 restraints weight = 13191.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161815 restraints weight = 11522.209| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15648 Z= 0.165 Angle : 0.572 7.700 21228 Z= 0.300 Chirality : 0.045 0.163 2424 Planarity : 0.005 0.048 2748 Dihedral : 6.726 84.917 2136 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.99 % Rotamer: Outliers : 1.32 % Allowed : 13.13 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1896 helix: 2.26 (0.21), residues: 645 sheet: -1.23 (0.26), residues: 322 loop : -0.67 (0.23), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 199 TYR 0.008 0.001 TYR P 43 PHE 0.010 0.001 PHE L 95 TRP 0.005 0.001 TRP L 154 HIS 0.004 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00379 (15648) covalent geometry : angle 0.57185 (21228) hydrogen bonds : bond 0.04503 ( 642) hydrogen bonds : angle 5.23729 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 337 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7885 (tmm) cc_final: 0.7462 (tmm) REVERT: K 17 LYS cc_start: 0.4069 (ptpt) cc_final: 0.2600 (tttp) REVERT: K 59 ARG cc_start: 0.7870 (mtp180) cc_final: 0.6907 (ptm160) REVERT: K 199 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7597 (ttp80) REVERT: M 135 ARG cc_start: 0.7212 (ptp-110) cc_final: 0.5413 (tpt-90) REVERT: O 1 MET cc_start: 0.7502 (tmm) cc_final: 0.6195 (tmm) REVERT: R 157 ASN cc_start: 0.8534 (t0) cc_final: 0.8319 (t0) REVERT: S 192 ASP cc_start: 0.7359 (m-30) cc_final: 0.7124 (m-30) outliers start: 22 outliers final: 17 residues processed: 346 average time/residue: 0.3103 time to fit residues: 154.7844 Evaluate side-chains 347 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN T 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.192275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155212 restraints weight = 78376.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159643 restraints weight = 30682.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162066 restraints weight = 17563.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163392 restraints weight = 13151.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.163870 restraints weight = 11465.749| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15648 Z= 0.119 Angle : 0.545 7.282 21228 Z= 0.285 Chirality : 0.044 0.167 2424 Planarity : 0.005 0.062 2748 Dihedral : 6.480 82.559 2136 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 1.32 % Allowed : 13.49 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1896 helix: 2.54 (0.21), residues: 652 sheet: -1.17 (0.26), residues: 329 loop : -0.58 (0.23), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 199 TYR 0.017 0.001 TYR I 3 PHE 0.009 0.001 PHE M 81 TRP 0.003 0.001 TRP I 154 HIS 0.004 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00267 (15648) covalent geometry : angle 0.54536 (21228) hydrogen bonds : bond 0.03833 ( 642) hydrogen bonds : angle 4.90452 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 346 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6547 (tp30) REVERT: I 5 THR cc_start: 0.9466 (p) cc_final: 0.9216 (t) REVERT: J 127 MET cc_start: 0.7851 (mpp) cc_final: 0.6805 (mtp) REVERT: K 199 ARG cc_start: 0.7811 (tmm-80) cc_final: 0.7575 (ttp80) REVERT: M 135 ARG cc_start: 0.7178 (ptp-110) cc_final: 0.5325 (tpt-90) REVERT: N 2 ASN cc_start: 0.8507 (t0) cc_final: 0.8181 (p0) REVERT: O 199 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7288 (ttp80) REVERT: Q 2 ASN cc_start: 0.7866 (p0) cc_final: 0.7652 (p0) REVERT: S 192 ASP cc_start: 0.7328 (m-30) cc_final: 0.7123 (m-30) outliers start: 22 outliers final: 12 residues processed: 357 average time/residue: 0.2983 time to fit residues: 154.7323 Evaluate side-chains 345 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 332 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 2 ASN L 2 ASN T 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.188778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151169 restraints weight = 79633.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155449 restraints weight = 32009.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157782 restraints weight = 18683.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159029 restraints weight = 14153.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159629 restraints weight = 12400.594| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15648 Z= 0.217 Angle : 0.604 7.263 21228 Z= 0.318 Chirality : 0.046 0.164 2424 Planarity : 0.006 0.048 2748 Dihedral : 6.784 84.221 2136 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 1.62 % Allowed : 14.75 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1896 helix: 2.10 (0.21), residues: 658 sheet: -1.21 (0.26), residues: 347 loop : -0.79 (0.23), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 199 TYR 0.013 0.001 TYR K 43 PHE 0.012 0.001 PHE P 95 TRP 0.007 0.001 TRP L 154 HIS 0.005 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00499 (15648) covalent geometry : angle 0.60357 (21228) hydrogen bonds : bond 0.04745 ( 642) hydrogen bonds : angle 5.23105 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 330 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 164 MET cc_start: 0.4853 (ttt) cc_final: 0.2485 (ppp) REVERT: K 1 MET cc_start: 0.7691 (tmm) cc_final: 0.7015 (tmm) REVERT: K 199 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7599 (ttp80) REVERT: M 135 ARG cc_start: 0.7179 (ptp-110) cc_final: 0.5238 (tpt-90) REVERT: N 2 ASN cc_start: 0.8550 (t0) cc_final: 0.8204 (p0) REVERT: O 199 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7383 (ttp80) REVERT: P 146 MET cc_start: 0.8572 (tpp) cc_final: 0.8365 (mmm) outliers start: 27 outliers final: 19 residues processed: 340 average time/residue: 0.2957 time to fit residues: 146.6889 Evaluate side-chains 342 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 2 ASN Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 178 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN L 2 ASN Q 2 ASN R 2 ASN T 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.192446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155092 restraints weight = 78780.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159524 restraints weight = 31027.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161969 restraints weight = 17865.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163258 restraints weight = 13402.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.163892 restraints weight = 11690.493| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15648 Z= 0.100 Angle : 0.538 6.389 21228 Z= 0.277 Chirality : 0.044 0.159 2424 Planarity : 0.005 0.048 2748 Dihedral : 6.379 81.303 2136 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 1.20 % Allowed : 15.71 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1896 helix: 2.65 (0.21), residues: 652 sheet: -1.10 (0.27), residues: 330 loop : -0.55 (0.24), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 199 TYR 0.019 0.001 TYR L 3 PHE 0.008 0.001 PHE P 95 TRP 0.005 0.001 TRP P 154 HIS 0.004 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00229 (15648) covalent geometry : angle 0.53782 (21228) hydrogen bonds : bond 0.03522 ( 642) hydrogen bonds : angle 4.70238 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 340 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 GLU cc_start: 0.7489 (tp30) cc_final: 0.6959 (tp30) REVERT: J 164 MET cc_start: 0.4586 (ttt) cc_final: 0.3715 (ttm) REVERT: K 1 MET cc_start: 0.7587 (tmm) cc_final: 0.6892 (tmm) REVERT: L 164 MET cc_start: 0.3672 (mtp) cc_final: 0.3014 (ttm) REVERT: M 135 ARG cc_start: 0.7164 (ptp-110) cc_final: 0.5218 (tpt-90) REVERT: N 2 ASN cc_start: 0.8518 (t0) cc_final: 0.8231 (p0) REVERT: Q 70 SER cc_start: 0.7099 (OUTLIER) cc_final: 0.6840 (p) outliers start: 20 outliers final: 13 residues processed: 351 average time/residue: 0.2874 time to fit residues: 147.0526 Evaluate side-chains 342 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 328 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 2 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 ASN M 125 GLN Q 2 ASN ** T 2 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 = 0.4209 r_free = 0.4209 target = 0.189343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151932 restraints weight = 78924.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156257 restraints weight = 31138.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158640 restraints weight = 17952.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159748 restraints weight = 13481.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.160480 restraints weight = 11848.840| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15648 Z= 0.205 Angle : 0.586 6.624 21228 Z= 0.307 Chirality : 0.045 0.162 2424 Planarity : 0.006 0.067 2748 Dihedral : 6.643 84.512 2136 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 1.20 % Allowed : 16.01 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1896 helix: 2.29 (0.21), residues: 658 sheet: -1.14 (0.26), residues: 348 loop : -0.74 (0.24), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 199 TYR 0.017 0.001 TYR K 43 PHE 0.011 0.001 PHE P 95 TRP 0.007 0.001 TRP L 154 HIS 0.004 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00473 (15648) covalent geometry : angle 0.58643 (21228) hydrogen bonds : bond 0.04327 ( 642) hydrogen bonds : angle 5.01556 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 329 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 GLU cc_start: 0.7360 (tp30) cc_final: 0.6863 (tp30) REVERT: J 164 MET cc_start: 0.4796 (ttt) cc_final: 0.3873 (ttm) REVERT: K 1 MET cc_start: 0.7649 (tmm) cc_final: 0.6910 (tmm) REVERT: L 71 GLN cc_start: 0.8205 (mp10) cc_final: 0.8000 (mp10) REVERT: L 164 MET cc_start: 0.3657 (mtp) cc_final: 0.3022 (ttm) REVERT: M 135 ARG cc_start: 0.7181 (ptp-110) cc_final: 0.5232 (tpt-90) REVERT: N 1 MET cc_start: 0.8762 (tmm) cc_final: 0.8273 (tmm) REVERT: N 2 ASN cc_start: 0.8552 (t0) cc_final: 0.8290 (p0) REVERT: Q 70 SER cc_start: 0.6524 (OUTLIER) cc_final: 0.6204 (p) REVERT: T 71 GLN cc_start: 0.8272 (mp10) cc_final: 0.7889 (mp10) outliers start: 20 outliers final: 16 residues processed: 340 average time/residue: 0.2830 time to fit residues: 139.5858 Evaluate side-chains 343 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 326 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN J 2 ASN K 191 GLN L 2 ASN Q 2 ASN T 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154577 restraints weight = 78766.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158969 restraints weight = 30945.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161371 restraints weight = 17793.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162476 restraints weight = 13359.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163233 restraints weight = 11738.365| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15648 Z= 0.105 Angle : 0.544 8.155 21228 Z= 0.279 Chirality : 0.044 0.162 2424 Planarity : 0.005 0.056 2748 Dihedral : 6.375 81.889 2136 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 1.38 % Allowed : 16.07 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1896 helix: 2.67 (0.21), residues: 652 sheet: -1.05 (0.26), residues: 348 loop : -0.55 (0.24), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 134 TYR 0.013 0.001 TYR K 43 PHE 0.008 0.001 PHE P 95 TRP 0.004 0.001 TRP I 154 HIS 0.004 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00247 (15648) covalent geometry : angle 0.54374 (21228) hydrogen bonds : bond 0.03529 ( 642) hydrogen bonds : angle 4.63657 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 337 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 GLU cc_start: 0.7444 (tp30) cc_final: 0.6951 (tp30) REVERT: J 164 MET cc_start: 0.4683 (ttt) cc_final: 0.3774 (ttm) REVERT: K 1 MET cc_start: 0.7581 (tmm) cc_final: 0.6867 (tmm) REVERT: L 71 GLN cc_start: 0.8190 (mp10) cc_final: 0.7978 (mp10) REVERT: L 164 MET cc_start: 0.3524 (mtp) cc_final: 0.2971 (ttm) REVERT: M 135 ARG cc_start: 0.7169 (ptp-110) cc_final: 0.5221 (tpt-90) REVERT: N 1 MET cc_start: 0.8718 (tmm) cc_final: 0.8308 (tmm) REVERT: N 2 ASN cc_start: 0.8508 (t0) cc_final: 0.8292 (p0) REVERT: N 9 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8655 (mp) REVERT: P 199 ARG cc_start: 0.7937 (tmm160) cc_final: 0.7640 (ptt-90) REVERT: Q 70 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.6157 (p) REVERT: T 71 GLN cc_start: 0.8262 (mp10) cc_final: 0.7927 (mp10) outliers start: 23 outliers final: 18 residues processed: 350 average time/residue: 0.3001 time to fit residues: 151.6284 Evaluate side-chains 353 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 333 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain J residue 2 ASN Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 2 ASN Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN ** J 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.154079 restraints weight = 78829.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158457 restraints weight = 31503.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160877 restraints weight = 18288.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162141 restraints weight = 13776.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162607 restraints weight = 12041.780| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 15648 Z= 0.319 Angle : 1.105 59.187 21228 Z= 0.714 Chirality : 0.050 0.580 2424 Planarity : 0.007 0.139 2748 Dihedral : 6.422 81.921 2136 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.80 % Favored : 94.04 % Rotamer: Outliers : 1.14 % Allowed : 16.25 % Favored : 82.61 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1896 helix: 2.67 (0.21), residues: 652 sheet: -1.04 (0.26), residues: 348 loop : -0.56 (0.24), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 199 TYR 0.042 0.001 TYR K 43 PHE 0.008 0.001 PHE P 95 TRP 0.003 0.001 TRP S 154 HIS 0.004 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00621 (15648) covalent geometry : angle 1.10503 (21228) hydrogen bonds : bond 0.03609 ( 642) hydrogen bonds : angle 4.65273 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 329 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 GLU cc_start: 0.7450 (tp30) cc_final: 0.6937 (tp30) REVERT: J 164 MET cc_start: 0.4719 (ttt) cc_final: 0.3805 (ttm) REVERT: L 164 MET cc_start: 0.3569 (mtp) cc_final: 0.3006 (ttm) REVERT: M 135 ARG cc_start: 0.7171 (ptp-110) cc_final: 0.5219 (tpt-90) REVERT: N 1 MET cc_start: 0.8719 (tmm) cc_final: 0.8310 (tmm) REVERT: N 2 ASN cc_start: 0.8503 (t0) cc_final: 0.8293 (p0) REVERT: N 9 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8642 (mp) REVERT: O 199 ARG cc_start: 0.7248 (ttp80) cc_final: 0.7011 (ttp80) REVERT: P 199 ARG cc_start: 0.7929 (tmm160) cc_final: 0.7639 (ptt-90) REVERT: Q 70 SER cc_start: 0.6465 (OUTLIER) cc_final: 0.6143 (p) REVERT: T 71 GLN cc_start: 0.8250 (mp10) cc_final: 0.7905 (mp10) outliers start: 19 outliers final: 15 residues processed: 339 average time/residue: 0.2919 time to fit residues: 143.4147 Evaluate side-chains 345 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 GLN Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 10.0000 chunk 25 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.191640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154165 restraints weight = 78966.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158548 restraints weight = 31278.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160973 restraints weight = 18107.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162229 restraints weight = 13606.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.162708 restraints weight = 11892.598| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 15648 Z= 0.319 Angle : 1.105 59.187 21228 Z= 0.714 Chirality : 0.050 0.580 2424 Planarity : 0.007 0.139 2748 Dihedral : 6.422 81.921 2136 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.80 % Favored : 94.04 % Rotamer: Outliers : 1.02 % Allowed : 16.37 % Favored : 82.61 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1896 helix: 2.67 (0.21), residues: 652 sheet: -1.04 (0.26), residues: 348 loop : -0.56 (0.24), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 199 TYR 0.042 0.001 TYR K 43 PHE 0.008 0.001 PHE P 95 TRP 0.003 0.001 TRP S 154 HIS 0.004 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00621 (15648) covalent geometry : angle 1.10503 (21228) hydrogen bonds : bond 0.03609 ( 642) hydrogen bonds : angle 4.65273 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.12 seconds wall clock time: 95 minutes 43.61 seconds (5743.61 seconds total)