Starting phenix.real_space_refine on Wed Oct 28 02:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sze_55367/10_2026/9sze_55367.map" } resolution = 3.05 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 16893 2.51 5 N 4410 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26622 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "E" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2981 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 374} Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 148 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "J" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "K" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2981 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 374} Chain: "L" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 148 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain: "M" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "N" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "O" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "P" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "Q" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2981 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 374} Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 148 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Time building chain proxies: 5.61, per 1000 atoms: 0.21 Number of scatterers: 26622 At special positions: 0 Unit cell: (128.412, 121.365, 140.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 5220 8.00 N 4410 7.00 C 16893 6.00 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6258 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 14.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.235A pdb=" N ALA A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.158A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.949A pdb=" N GLN E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.684A pdb=" N GLY E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 170 through 174 removed outlier: 6.723A pdb=" N ASN E 174 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 Processing helix chain 'E' and resid 232 through 240 removed outlier: 4.499A pdb=" N ALA E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 346 removed outlier: 3.666A pdb=" N GLN E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'G' and resid 78 through 85 Processing helix chain 'G' and resid 190 through 201 Processing helix chain 'G' and resid 207 through 214 removed outlier: 4.235A pdb=" N ALA G 212 " --> pdb=" O PRO G 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 190 through 200 Processing helix chain 'H' and resid 207 through 214 removed outlier: 4.159A pdb=" N ALA H 212 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY H 213 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'K' and resid 17 through 21 Processing helix chain 'K' and resid 62 through 69 removed outlier: 3.950A pdb=" N GLN K 66 " --> pdb=" O ASP K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 96 No H-bonds generated for 'chain 'K' and resid 94 through 96' Processing helix chain 'K' and resid 120 through 128 removed outlier: 3.684A pdb=" N GLY K 124 " --> pdb=" O SER K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 137 Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 170 through 174 removed outlier: 6.723A pdb=" N ASN K 174 " --> pdb=" O ALA K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 199 Processing helix chain 'K' and resid 232 through 240 removed outlier: 4.500A pdb=" N ALA K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 346 removed outlier: 3.665A pdb=" N GLN K 346 " --> pdb=" O LYS K 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 749 through 760 Processing helix chain 'M' and resid 78 through 85 Processing helix chain 'M' and resid 190 through 201 Processing helix chain 'M' and resid 207 through 214 removed outlier: 4.235A pdb=" N ALA M 212 " --> pdb=" O PRO M 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY M 213 " --> pdb=" O SER M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 86 Processing helix chain 'N' and resid 190 through 200 Processing helix chain 'N' and resid 207 through 214 removed outlier: 4.159A pdb=" N ALA N 212 " --> pdb=" O PRO N 208 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY N 213 " --> pdb=" O SER N 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 39 Processing helix chain 'P' and resid 147 through 153 Processing helix chain 'Q' and resid 17 through 21 Processing helix chain 'Q' and resid 62 through 69 removed outlier: 3.950A pdb=" N GLN Q 66 " --> pdb=" O ASP Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 96 No H-bonds generated for 'chain 'Q' and resid 94 through 96' Processing helix chain 'Q' and resid 120 through 128 removed outlier: 3.684A pdb=" N GLY Q 124 " --> pdb=" O SER Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 137 Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 170 through 174 removed outlier: 6.723A pdb=" N ASN Q 174 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 199 Processing helix chain 'Q' and resid 232 through 240 removed outlier: 4.499A pdb=" N ALA Q 236 " --> pdb=" O LEU Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 346 removed outlier: 3.666A pdb=" N GLN Q 346 " --> pdb=" O LYS Q 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 749 through 760 Processing sheet with id=1, first strand: chain 'A' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 26 through 27 current: chain 'A' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 73 current: chain 'A' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 136 current: chain 'A' and resid 157 through 164 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 164 current: chain 'B' and resid 98 through 101 Processing sheet with id=2, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.968A pdb=" N MET A 59 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 88 through 91 removed outlier: 4.028A pdb=" N ALA A 98 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 166 through 171 removed outlier: 5.316A pdb=" N ALA A 169 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 26 through 27 current: chain 'B' and resid 65 through 73 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 65 through 73 current: chain 'B' and resid 124 through 136 removed outlier: 4.165A pdb=" N SER B 133 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=7, first strand: chain 'B' and resid 166 through 171 removed outlier: 5.365A pdb=" N ALA B 169 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 22 through 23 current: chain 'C' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 51 current: chain 'C' and resid 80 through 83 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 80 through 83 current: chain 'C' and resid 97 through 103 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 97 through 103 current: chain 'C' and resid 116 through 119 Processing sheet with id=9, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.060A pdb=" N LEU D 14 " --> pdb=" O ALA D 4 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 26 through 32 current: chain 'D' and resid 60 through 66 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 66 current: chain 'D' and resid 84 through 91 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 91 current: chain 'D' and resid 156 through 160 removed outlier: 6.717A pdb=" N PHE D 165 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D 159 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 113 through 118 removed outlier: 5.869A pdb=" N THR D 115 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE D 185 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 4 through 10 removed outlier: 3.555A pdb=" N HIS E 4 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU E 42 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP E 31 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU E 40 " --> pdb=" O ASP E 31 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP E 33 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY E 38 " --> pdb=" O TRP E 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 44 current: chain 'E' and resid 75 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 87 through 92 current: chain 'E' and resid 348 through 350 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 348 through 350 current: chain 'E' and resid 376 through 382 Processing sheet with id=12, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.684A pdb=" N ILE E 104 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'E' and resid 111 through 113 Processing sheet with id=14, first strand: chain 'E' and resid 152 through 153 removed outlier: 6.368A pdb=" N SER E 153 " --> pdb=" O TYR E 221 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.617A pdb=" N LEU E 372 " --> pdb=" O THR E 364 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 291 through 299 removed outlier: 4.251A pdb=" N GLY E 298 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR E 278 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL E 264 " --> pdb=" O TYR E 314 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ILE E 316 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA E 266 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'G' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 26 through 27 current: chain 'G' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 73 current: chain 'G' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 124 through 136 current: chain 'G' and resid 157 through 164 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 157 through 164 current: chain 'H' and resid 98 through 101 Processing sheet with id=18, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.969A pdb=" N MET G 59 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'G' and resid 88 through 91 removed outlier: 4.028A pdb=" N ALA G 98 " --> pdb=" O ILE G 91 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'G' and resid 166 through 171 removed outlier: 5.316A pdb=" N ALA G 169 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'H' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 26 through 27 current: chain 'H' and resid 65 through 73 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 65 through 73 current: chain 'H' and resid 124 through 136 removed outlier: 4.166A pdb=" N SER H 133 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 48 through 52 Processing sheet with id=23, first strand: chain 'H' and resid 166 through 171 removed outlier: 5.365A pdb=" N ALA H 169 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 22 through 23 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 51 current: chain 'I' and resid 80 through 83 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 80 through 83 current: chain 'I' and resid 97 through 103 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 97 through 103 current: chain 'I' and resid 116 through 119 Processing sheet with id=25, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.060A pdb=" N LEU J 14 " --> pdb=" O ALA J 4 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 26 through 32 current: chain 'J' and resid 60 through 66 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 60 through 66 current: chain 'J' and resid 84 through 91 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 84 through 91 current: chain 'J' and resid 156 through 160 removed outlier: 6.716A pdb=" N PHE J 165 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL J 159 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'J' and resid 113 through 118 removed outlier: 5.869A pdb=" N THR J 115 " --> pdb=" O ILE J 185 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE J 185 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 4 through 10 removed outlier: 3.554A pdb=" N HIS K 4 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU K 42 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP K 31 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU K 40 " --> pdb=" O ASP K 31 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP K 33 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY K 38 " --> pdb=" O TRP K 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 38 through 44 current: chain 'K' and resid 75 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 87 through 92 current: chain 'K' and resid 348 through 350 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 348 through 350 current: chain 'K' and resid 376 through 382 Processing sheet with id=28, first strand: chain 'K' and resid 104 through 105 removed outlier: 3.684A pdb=" N ILE K 104 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 111 through 113 Processing sheet with id=30, first strand: chain 'K' and resid 152 through 153 removed outlier: 6.368A pdb=" N SER K 153 " --> pdb=" O TYR K 221 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'K' and resid 226 through 230 removed outlier: 6.617A pdb=" N LEU K 372 " --> pdb=" O THR K 364 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 291 through 299 removed outlier: 4.250A pdb=" N GLY K 298 " --> pdb=" O TYR K 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR K 278 " --> pdb=" O GLY K 298 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL K 264 " --> pdb=" O TYR K 314 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ILE K 316 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA K 266 " --> pdb=" O ILE K 316 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'M' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 26 through 27 current: chain 'M' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 66 through 73 current: chain 'M' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 124 through 136 current: chain 'M' and resid 157 through 164 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 157 through 164 current: chain 'N' and resid 98 through 101 Processing sheet with id=34, first strand: chain 'M' and resid 47 through 51 removed outlier: 6.969A pdb=" N MET M 59 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'M' and resid 88 through 91 removed outlier: 4.028A pdb=" N ALA M 98 " --> pdb=" O ILE M 91 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'M' and resid 166 through 171 removed outlier: 5.316A pdb=" N ALA M 169 " --> pdb=" O ARG M 176 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'N' and resid 9 through 23 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 26 through 27 current: chain 'N' and resid 65 through 73 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 65 through 73 current: chain 'N' and resid 124 through 136 removed outlier: 4.166A pdb=" N SER N 133 " --> pdb=" O GLN N 164 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'N' and resid 48 through 52 Processing sheet with id=39, first strand: chain 'N' and resid 166 through 171 removed outlier: 5.364A pdb=" N ALA N 169 " --> pdb=" O ARG N 176 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 23 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 45 through 51 current: chain 'O' and resid 80 through 83 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 80 through 83 current: chain 'O' and resid 97 through 103 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 97 through 103 current: chain 'O' and resid 116 through 119 Processing sheet with id=41, first strand: chain 'P' and resid 2 through 6 removed outlier: 4.061A pdb=" N LEU P 14 " --> pdb=" O ALA P 4 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 26 through 32 current: chain 'P' and resid 60 through 66 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 60 through 66 current: chain 'P' and resid 84 through 91 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 84 through 91 current: chain 'P' and resid 156 through 160 removed outlier: 6.716A pdb=" N PHE P 165 " --> pdb=" O PHE P 157 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL P 159 " --> pdb=" O SER P 163 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'P' and resid 113 through 118 removed outlier: 5.870A pdb=" N THR P 115 " --> pdb=" O ILE P 185 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE P 185 " --> pdb=" O THR P 115 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'Q' and resid 4 through 10 removed outlier: 3.555A pdb=" N HIS Q 4 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU Q 42 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP Q 31 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU Q 40 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP Q 33 " --> pdb=" O GLY Q 38 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY Q 38 " --> pdb=" O TRP Q 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 38 through 44 current: chain 'Q' and resid 75 through 82 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 87 through 92 current: chain 'Q' and resid 348 through 350 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 348 through 350 current: chain 'Q' and resid 376 through 382 Processing sheet with id=44, first strand: chain 'Q' and resid 104 through 105 removed outlier: 3.685A pdb=" N ILE Q 104 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'Q' and resid 111 through 113 Processing sheet with id=46, first strand: chain 'Q' and resid 152 through 153 removed outlier: 6.368A pdb=" N SER Q 153 " --> pdb=" O TYR Q 221 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'Q' and resid 226 through 230 removed outlier: 6.617A pdb=" N LEU Q 372 " --> pdb=" O THR Q 364 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 291 through 299 removed outlier: 4.251A pdb=" N GLY Q 298 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR Q 278 " --> pdb=" O GLY Q 298 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL Q 264 " --> pdb=" O TYR Q 314 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ILE Q 316 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA Q 266 " --> pdb=" O ILE Q 316 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1341 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: 5.30 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8643 1.34 - 1.46: 5945 1.46 - 1.58: 12430 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 27186 Sorted by residual: bond pdb=" CA ASN E 142 " pdb=" CB ASN E 142 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.35e-01 bond pdb=" CA ASN K 142 " pdb=" CB ASN K 142 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.26e-01 bond pdb=" CA ASN Q 142 " pdb=" CB ASN Q 142 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.09e-01 bond pdb=" C ASP N 120 " pdb=" N PRO N 121 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.56e-01 bond pdb=" CA GLY B 136 " pdb=" C GLY B 136 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.29e-02 6.01e+03 4.54e-01 ... (remaining 27181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 36411 1.22 - 2.44: 257 2.44 - 3.65: 157 3.65 - 4.87: 12 4.87 - 6.09: 9 Bond angle restraints: 36846 Sorted by residual: angle pdb=" C ALA K 141 " pdb=" N ASN K 142 " pdb=" CA ASN K 142 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C ALA Q 141 " pdb=" N ASN Q 142 " pdb=" CA ASN Q 142 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C ALA E 141 " pdb=" N ASN E 142 " pdb=" CA ASN E 142 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.16e+00 angle pdb=" C GLN C 59 " pdb=" N GLU C 60 " pdb=" CA GLU C 60 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" C GLN O 59 " pdb=" N GLU O 60 " pdb=" CA GLU O 60 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.38e+00 ... (remaining 36841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 14877 16.00 - 31.99: 960 31.99 - 47.99: 138 47.99 - 63.98: 60 63.98 - 79.98: 9 Dihedral angle restraints: 16044 sinusoidal: 6183 harmonic: 9861 Sorted by residual: dihedral pdb=" CA ARG D 196 " pdb=" CB ARG D 196 " pdb=" CG ARG D 196 " pdb=" CD ARG D 196 " ideal model delta sinusoidal sigma weight residual 180.00 120.92 59.08 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG J 196 " pdb=" CB ARG J 196 " pdb=" CG ARG J 196 " pdb=" CD ARG J 196 " ideal model delta sinusoidal sigma weight residual 180.00 120.93 59.07 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG P 196 " pdb=" CB ARG P 196 " pdb=" CG ARG P 196 " pdb=" CD ARG P 196 " ideal model delta sinusoidal sigma weight residual 180.00 120.96 59.04 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 16041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2529 0.028 - 0.056: 980 0.056 - 0.084: 213 0.084 - 0.111: 279 0.111 - 0.139: 97 Chirality restraints: 4098 Sorted by residual: chirality pdb=" CA ASN E 142 " pdb=" N ASN E 142 " pdb=" C ASN E 142 " pdb=" CB ASN E 142 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ASN K 142 " pdb=" N ASN K 142 " pdb=" C ASN K 142 " pdb=" CB ASN K 142 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ASN Q 142 " pdb=" N ASN Q 142 " pdb=" C ASN Q 142 " pdb=" CB ASN Q 142 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 4095 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU O 41 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO O 42 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO O 42 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO O 42 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 41 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 42 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 41 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO I 42 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 42 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 42 " -0.019 5.00e-02 4.00e+02 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8996 2.84 - 3.35: 22461 3.35 - 3.87: 46043 3.87 - 4.38: 54738 4.38 - 4.90: 93230 Nonbonded interactions: 225468 Sorted by model distance: nonbonded pdb=" OD1 ASP A 197 " pdb=" OG1 THR A 201 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASP G 197 " pdb=" OG1 THR G 201 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP M 197 " pdb=" OG1 THR M 201 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR Q 364 " pdb=" OG1 THR Q 374 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR K 364 " pdb=" OG1 THR K 374 " model vdw 2.364 3.040 ... (remaining 225463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.440 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.350 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 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 : 0.002 0.024 27186 Z= 0.076 Angle : 0.386 6.089 36846 Z= 0.205 Chirality : 0.042 0.139 4098 Planarity : 0.003 0.034 4770 Dihedral : 11.062 79.980 9786 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3429 helix: 1.34 (0.28), residues: 360 sheet: 0.22 (0.16), residues: 1188 loop : -0.41 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 166 TYR 0.007 0.001 TYR O 100 PHE 0.011 0.001 PHE K 310 TRP 0.005 0.001 TRP K 76 HIS 0.001 0.000 HIS Q 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00158 / 0.08 (27186) covalent geometry : angle 0.38600 / 0.21 (36846) hydrogen bonds : bond 0.23717 / 16.14 ( 489) hydrogen bonds : angle 7.87468 / 5.38 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 831 time to evaluate : 0.854 Fit side-chains REVERT: A 41 LYS cc_start: 0.8554 (tttt) cc_final: 0.8279 (ttmm) REVERT: A 55 ASP cc_start: 0.7902 (m-30) cc_final: 0.7571 (m-30) REVERT: A 70 GLU cc_start: 0.7770 (tt0) cc_final: 0.7497 (tt0) REVERT: A 82 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8259 (mtmt) REVERT: A 147 ASP cc_start: 0.7460 (t0) cc_final: 0.7206 (t0) REVERT: A 180 GLU cc_start: 0.8009 (tt0) cc_final: 0.7753 (pt0) REVERT: B 97 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7968 (tp30) REVERT: B 151 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6725 (mm-30) REVERT: B 153 SER cc_start: 0.8615 (m) cc_final: 0.8411 (m) REVERT: C 7 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8065 (mtpt) REVERT: C 92 ARG cc_start: 0.8492 (ttt90) cc_final: 0.7447 (ttt180) REVERT: D 13 ASP cc_start: 0.8299 (m-30) cc_final: 0.7988 (t0) REVERT: D 102 VAL cc_start: 0.8845 (t) cc_final: 0.8470 (m) REVERT: D 190 ASP cc_start: 0.7181 (p0) cc_final: 0.6794 (p0) REVERT: D 200 ILE cc_start: 0.8521 (mt) cc_final: 0.8149 (mt) REVERT: E 174 ASN cc_start: 0.7509 (p0) cc_final: 0.6769 (t0) REVERT: E 234 MET cc_start: 0.7503 (tmm) cc_final: 0.6758 (tmm) REVERT: E 271 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6835 (tp30) REVERT: G 26 VAL cc_start: 0.8858 (t) cc_final: 0.8646 (p) REVERT: G 42 LYS cc_start: 0.8234 (tttt) cc_final: 0.7922 (pttp) REVERT: G 55 ASP cc_start: 0.7899 (m-30) cc_final: 0.7685 (m-30) REVERT: G 82 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8039 (mtmt) REVERT: G 147 ASP cc_start: 0.7518 (t0) cc_final: 0.7233 (t0) REVERT: G 180 GLU cc_start: 0.7893 (tt0) cc_final: 0.7646 (pt0) REVERT: I 92 ARG cc_start: 0.8393 (ttt90) cc_final: 0.7184 (ttt180) REVERT: J 1 MET cc_start: 0.7853 (pp-130) cc_final: 0.7297 (pp-130) REVERT: J 13 ASP cc_start: 0.8374 (m-30) cc_final: 0.8021 (t0) REVERT: J 18 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7420 (mt-10) REVERT: J 102 VAL cc_start: 0.8807 (t) cc_final: 0.8446 (m) REVERT: J 120 ASP cc_start: 0.7426 (m-30) cc_final: 0.7135 (m-30) REVERT: J 147 ASP cc_start: 0.6573 (p0) cc_final: 0.5844 (t0) REVERT: J 190 ASP cc_start: 0.7157 (p0) cc_final: 0.6761 (p0) REVERT: K 178 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7081 (mm-40) REVERT: K 234 MET cc_start: 0.7433 (tmm) cc_final: 0.6399 (tmm) REVERT: K 312 GLU cc_start: 0.8561 (pm20) cc_final: 0.8276 (pm20) REVERT: M 41 LYS cc_start: 0.8663 (tttt) cc_final: 0.8407 (tttp) REVERT: M 42 LYS cc_start: 0.8328 (tttt) cc_final: 0.7977 (ptmt) REVERT: M 82 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8143 (mtmt) REVERT: M 97 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7709 (tt0) REVERT: M 147 ASP cc_start: 0.7466 (t0) cc_final: 0.7236 (t0) REVERT: N 9 THR cc_start: 0.8598 (m) cc_final: 0.8372 (p) REVERT: N 97 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8038 (tp30) REVERT: N 180 GLU cc_start: 0.7751 (tt0) cc_final: 0.7542 (tt0) REVERT: O 7 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8040 (mtpt) REVERT: P 13 ASP cc_start: 0.8196 (m-30) cc_final: 0.7909 (t0) REVERT: P 18 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7314 (mt-10) REVERT: P 102 VAL cc_start: 0.8843 (t) cc_final: 0.8537 (m) REVERT: P 147 ASP cc_start: 0.6554 (p0) cc_final: 0.5870 (t0) REVERT: P 169 MET cc_start: 0.8880 (ttm) cc_final: 0.8492 (ttm) REVERT: P 190 ASP cc_start: 0.7198 (p0) cc_final: 0.6860 (p0) REVERT: Q 145 SER cc_start: 0.7901 (p) cc_final: 0.7690 (t) REVERT: Q 234 MET cc_start: 0.7480 (tmm) cc_final: 0.6715 (tmm) REVERT: Q 273 LEU cc_start: 0.7393 (mt) cc_final: 0.7188 (mt) outliers start: 2 outliers final: 0 residues processed: 833 average time/residue: 0.1825 time to fit residues: 231.7486 Evaluate side-chains 434 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN B 124 GLN D 45 GLN G 68 GLN G 115 GLN H 107 ASN H 124 GLN ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN N 124 GLN P 45 GLN P 137 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.092495 restraints weight = 38407.942| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.86 r_work: 0.2918 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27186 Z= 0.101 Angle : 0.446 5.222 36846 Z= 0.240 Chirality : 0.044 0.203 4098 Planarity : 0.003 0.038 4770 Dihedral : 3.895 58.651 3744 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.80 % Allowed : 11.33 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3429 helix: 1.84 (0.27), residues: 393 sheet: 0.26 (0.16), residues: 1197 loop : -0.43 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 186 TYR 0.012 0.001 TYR Q 207 PHE 0.014 0.001 PHE K 310 TRP 0.010 0.001 TRP E 265 HIS 0.002 0.000 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (27186) covalent geometry : angle 0.44642 / 0.24 (36846) hydrogen bonds : bond 0.03436 / 2.36 ( 489) hydrogen bonds : angle 5.42477 / 3.68 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 449 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7756 (t0) cc_final: 0.7504 (t0) REVERT: A 180 GLU cc_start: 0.8050 (tt0) cc_final: 0.7757 (pt0) REVERT: A 186 THR cc_start: 0.8097 (m) cc_final: 0.7852 (p) REVERT: B 95 ASP cc_start: 0.7471 (m-30) cc_final: 0.7121 (t0) REVERT: B 151 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6788 (mm-30) REVERT: C 7 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8340 (mtpt) REVERT: D 13 ASP cc_start: 0.8334 (m-30) cc_final: 0.8004 (t0) REVERT: D 102 VAL cc_start: 0.8888 (t) cc_final: 0.8543 (m) REVERT: D 119 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7623 (ttmm) REVERT: D 190 ASP cc_start: 0.7319 (p0) cc_final: 0.7102 (p0) REVERT: E 174 ASN cc_start: 0.7656 (p0) cc_final: 0.6850 (t0) REVERT: E 234 MET cc_start: 0.7624 (tmm) cc_final: 0.6894 (tmm) REVERT: F 763 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7395 (ttm-80) REVERT: G 26 VAL cc_start: 0.8797 (t) cc_final: 0.8571 (p) REVERT: G 42 LYS cc_start: 0.8495 (tttt) cc_final: 0.7966 (pttp) REVERT: G 147 ASP cc_start: 0.7739 (t0) cc_final: 0.7496 (t0) REVERT: G 180 GLU cc_start: 0.7946 (tt0) cc_final: 0.7657 (pt0) REVERT: G 186 THR cc_start: 0.7935 (m) cc_final: 0.7684 (p) REVERT: H 42 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8157 (mmtm) REVERT: H 151 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6721 (tt0) REVERT: I 112 MET cc_start: 0.8317 (ttm) cc_final: 0.7975 (ttm) REVERT: J 1 MET cc_start: 0.7809 (pp-130) cc_final: 0.7267 (pp-130) REVERT: J 13 ASP cc_start: 0.8255 (m-30) cc_final: 0.7878 (t0) REVERT: J 45 GLN cc_start: 0.8741 (mt0) cc_final: 0.8540 (mt0) REVERT: J 102 VAL cc_start: 0.8804 (t) cc_final: 0.8488 (m) REVERT: J 147 ASP cc_start: 0.6735 (p0) cc_final: 0.6140 (t0) REVERT: J 190 ASP cc_start: 0.7282 (p0) cc_final: 0.7029 (p0) REVERT: K 312 GLU cc_start: 0.8594 (pm20) cc_final: 0.8315 (pm20) REVERT: L 763 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7466 (ttm-80) REVERT: M 26 VAL cc_start: 0.8749 (t) cc_final: 0.8509 (p) REVERT: M 41 LYS cc_start: 0.8638 (tttt) cc_final: 0.8431 (tttp) REVERT: M 42 LYS cc_start: 0.8532 (tttt) cc_final: 0.8017 (pttp) REVERT: M 44 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7685 (tp30) REVERT: M 70 GLU cc_start: 0.8097 (tt0) cc_final: 0.7861 (tt0) REVERT: M 97 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7802 (tt0) REVERT: M 151 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7129 (pt0) REVERT: N 9 THR cc_start: 0.8692 (m) cc_final: 0.8372 (p) REVERT: N 95 ASP cc_start: 0.7503 (m-30) cc_final: 0.7056 (t0) REVERT: N 180 GLU cc_start: 0.8067 (tt0) cc_final: 0.7812 (pt0) REVERT: O 7 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8369 (mtpt) REVERT: P 1 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7067 (pp-130) REVERT: P 102 VAL cc_start: 0.8854 (t) cc_final: 0.8611 (m) REVERT: P 169 MET cc_start: 0.8630 (ttm) cc_final: 0.8167 (ttm) REVERT: P 190 ASP cc_start: 0.7246 (p0) cc_final: 0.7035 (p0) REVERT: Q 119 THR cc_start: 0.8279 (p) cc_final: 0.8065 (p) REVERT: Q 234 MET cc_start: 0.7487 (tmm) cc_final: 0.6950 (tmm) outliers start: 51 outliers final: 34 residues processed: 484 average time/residue: 0.1691 time to fit residues: 129.4729 Evaluate side-chains 435 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 400 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 33 ASP Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [20, 234, 173, 340, 330, 249, 24, 204, 213, 321, 293] chunk 20 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 173 optimal weight: 0.0270 chunk 340 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 204 optimal weight: 0.0370 chunk 213 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 overall best weight: 1.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 45 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN J 137 GLN N 107 ASN P 45 GLN Q 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.089446 restraints weight = 38969.102| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.59 r_work: 0.2875 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27186 Z= 0.160 Angle : 0.493 5.619 36846 Z= 0.265 Chirality : 0.046 0.224 4098 Planarity : 0.004 0.041 4770 Dihedral : 4.347 48.858 3744 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.65 % Allowed : 11.83 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3429 helix: 1.65 (0.26), residues: 393 sheet: 0.39 (0.17), residues: 1026 loop : -0.60 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 127 TYR 0.020 0.001 TYR G 200 PHE 0.024 0.002 PHE K 201 TRP 0.011 0.001 TRP K 76 HIS 0.002 0.001 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (27186) covalent geometry : angle 0.49285 / 0.26 (36846) hydrogen bonds : bond 0.03732 / 2.57 ( 489) hydrogen bonds : angle 5.10706 / 3.47 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 0.953 Fit side-chains REVERT: B 95 ASP cc_start: 0.7571 (m-30) cc_final: 0.7287 (t0) REVERT: B 106 THR cc_start: 0.8726 (p) cc_final: 0.8471 (p) REVERT: C 7 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8367 (mtpt) REVERT: C 111 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: D 13 ASP cc_start: 0.8205 (m-30) cc_final: 0.7901 (t0) REVERT: D 102 VAL cc_start: 0.8833 (t) cc_final: 0.8534 (m) REVERT: E 174 ASN cc_start: 0.7722 (p0) cc_final: 0.6946 (t0) REVERT: E 234 MET cc_start: 0.7740 (tmm) cc_final: 0.7203 (tmm) REVERT: E 303 SER cc_start: 0.8590 (p) cc_final: 0.8389 (t) REVERT: F 756 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8422 (mtmt) REVERT: G 42 LYS cc_start: 0.8491 (tttt) cc_final: 0.7906 (pttp) REVERT: G 147 ASP cc_start: 0.7742 (t0) cc_final: 0.7487 (t0) REVERT: I 112 MET cc_start: 0.8415 (ttm) cc_final: 0.8155 (ttm) REVERT: J 1 MET cc_start: 0.7609 (pp-130) cc_final: 0.7103 (pp-130) REVERT: J 18 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7672 (mt-10) REVERT: J 102 VAL cc_start: 0.8763 (t) cc_final: 0.8492 (m) REVERT: J 147 ASP cc_start: 0.6811 (p0) cc_final: 0.6271 (t0) REVERT: K 312 GLU cc_start: 0.8575 (pm20) cc_final: 0.8289 (pm20) REVERT: M 26 VAL cc_start: 0.8714 (t) cc_final: 0.8454 (p) REVERT: M 42 LYS cc_start: 0.8508 (tttt) cc_final: 0.7970 (pttp) REVERT: M 70 GLU cc_start: 0.8007 (tt0) cc_final: 0.7725 (tt0) REVERT: M 151 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7110 (pt0) REVERT: M 187 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7492 (mtmm) REVERT: N 95 ASP cc_start: 0.7529 (m-30) cc_final: 0.7254 (t0) REVERT: N 106 THR cc_start: 0.8666 (p) cc_final: 0.8390 (p) REVERT: N 180 GLU cc_start: 0.8311 (tt0) cc_final: 0.8111 (tt0) REVERT: O 7 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8435 (mtpt) REVERT: O 41 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8339 (mm-30) REVERT: P 1 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6776 (pp-130) REVERT: P 18 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7599 (mt-10) REVERT: P 102 VAL cc_start: 0.8792 (t) cc_final: 0.8584 (m) REVERT: P 119 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7594 (ttmt) REVERT: P 151 LYS cc_start: 0.8732 (mttp) cc_final: 0.8514 (mttp) REVERT: P 169 MET cc_start: 0.8743 (ttm) cc_final: 0.8349 (ttm) REVERT: Q 119 THR cc_start: 0.8229 (p) cc_final: 0.7962 (p) REVERT: Q 234 MET cc_start: 0.7573 (tmm) cc_final: 0.6776 (tmm) outliers start: 75 outliers final: 57 residues processed: 457 average time/residue: 0.1706 time to fit residues: 123.9645 Evaluate side-chains 423 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 117 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [220, 330, 180, 149, 66, 183, 267, 214, 154, 193, 190] chunk 220 optimal weight: 4.9990 chunk 330 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 267 optimal weight: 6.9990 chunk 214 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.089053 restraints weight = 38943.617| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.59 r_work: 0.2873 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27186 Z= 0.134 Angle : 0.463 5.637 36846 Z= 0.249 Chirality : 0.045 0.171 4098 Planarity : 0.003 0.042 4770 Dihedral : 4.311 47.479 3744 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.04 % Allowed : 12.78 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3429 helix: 1.70 (0.26), residues: 393 sheet: 0.20 (0.17), residues: 1044 loop : -0.56 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 93 TYR 0.013 0.001 TYR K 207 PHE 0.021 0.001 PHE K 201 TRP 0.009 0.001 TRP E 265 HIS 0.002 0.000 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (27186) covalent geometry : angle 0.46258 / 0.25 (36846) hydrogen bonds : bond 0.03247 / 2.24 ( 489) hydrogen bonds : angle 4.96510 / 3.37 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 370 time to evaluate : 0.955 Fit side-chains REVERT: A 70 GLU cc_start: 0.8030 (tt0) cc_final: 0.7725 (tt0) REVERT: B 95 ASP cc_start: 0.7556 (m-30) cc_final: 0.7305 (t0) REVERT: B 106 THR cc_start: 0.8707 (p) cc_final: 0.8456 (p) REVERT: C 7 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8371 (mtpt) REVERT: C 111 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: D 102 VAL cc_start: 0.8864 (t) cc_final: 0.8602 (m) REVERT: D 119 LYS cc_start: 0.7933 (tmtt) cc_final: 0.7633 (ttmt) REVERT: E 174 ASN cc_start: 0.7687 (p0) cc_final: 0.6974 (t0) REVERT: E 234 MET cc_start: 0.7727 (tmm) cc_final: 0.7172 (tmm) REVERT: E 303 SER cc_start: 0.8578 (p) cc_final: 0.8367 (t) REVERT: F 756 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8507 (mtmt) REVERT: G 42 LYS cc_start: 0.8454 (tttt) cc_final: 0.7871 (pttp) REVERT: G 68 GLN cc_start: 0.8915 (mm110) cc_final: 0.8714 (mm-40) REVERT: G 147 ASP cc_start: 0.7751 (t0) cc_final: 0.7471 (t0) REVERT: H 42 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8235 (mmtt) REVERT: H 97 GLU cc_start: 0.8280 (tp30) cc_final: 0.8077 (mt-10) REVERT: H 210 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7985 (mt-10) REVERT: I 112 MET cc_start: 0.8450 (ttm) cc_final: 0.8226 (ttm) REVERT: J 1 MET cc_start: 0.7617 (pp-130) cc_final: 0.7117 (pp-130) REVERT: J 18 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7678 (mt-10) REVERT: J 102 VAL cc_start: 0.8769 (t) cc_final: 0.8509 (m) REVERT: J 147 ASP cc_start: 0.6800 (p0) cc_final: 0.6243 (t0) REVERT: K 312 GLU cc_start: 0.8651 (pm20) cc_final: 0.8397 (pm20) REVERT: M 26 VAL cc_start: 0.8692 (t) cc_final: 0.8446 (p) REVERT: M 42 LYS cc_start: 0.8527 (tttt) cc_final: 0.7960 (pttp) REVERT: M 97 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7896 (tt0) REVERT: N 95 ASP cc_start: 0.7597 (m-30) cc_final: 0.7350 (t0) REVERT: N 106 THR cc_start: 0.8696 (p) cc_final: 0.8404 (p) REVERT: O 7 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8406 (mtpt) REVERT: P 1 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6652 (pp-130) REVERT: P 18 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7540 (mt-10) REVERT: P 102 VAL cc_start: 0.8790 (t) cc_final: 0.8589 (m) REVERT: P 151 LYS cc_start: 0.8709 (mttp) cc_final: 0.8482 (mttp) REVERT: P 169 MET cc_start: 0.8741 (ttm) cc_final: 0.8326 (ttm) REVERT: Q 130 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8481 (m-40) REVERT: Q 234 MET cc_start: 0.7582 (tmm) cc_final: 0.7028 (tmm) outliers start: 86 outliers final: 67 residues processed: 432 average time/residue: 0.1673 time to fit residues: 115.1189 Evaluate side-chains 427 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 117 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 130 ASN Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [45, 62, 105, 69, 9, 316, 244, 325, 104, 223, 78] chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 223 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.086342 restraints weight = 39538.133| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.61 r_work: 0.2820 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 27186 Z= 0.264 Angle : 0.562 5.530 36846 Z= 0.304 Chirality : 0.049 0.173 4098 Planarity : 0.004 0.047 4770 Dihedral : 4.999 55.055 3744 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.46 % Allowed : 13.77 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3429 helix: 1.42 (0.27), residues: 357 sheet: -0.17 (0.15), residues: 1194 loop : -0.56 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 76 TYR 0.018 0.002 TYR A 200 PHE 0.020 0.002 PHE K 201 TRP 0.013 0.002 TRP K 76 HIS 0.003 0.001 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 (27186) covalent geometry : angle 0.56154 / 0.30 (36846) hydrogen bonds : bond 0.04293 / 2.95 ( 489) hydrogen bonds : angle 5.26602 / 3.61 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 344 time to evaluate : 0.858 Fit side-chains REVERT: A 70 GLU cc_start: 0.8168 (tt0) cc_final: 0.7961 (tt0) REVERT: B 106 THR cc_start: 0.8823 (p) cc_final: 0.8559 (p) REVERT: C 7 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8570 (mtpt) REVERT: C 111 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: E 174 ASN cc_start: 0.7744 (p0) cc_final: 0.7117 (t0) REVERT: E 234 MET cc_start: 0.7922 (tmm) cc_final: 0.7362 (tmm) REVERT: G 42 LYS cc_start: 0.8484 (tttt) cc_final: 0.8001 (pttp) REVERT: G 147 ASP cc_start: 0.7889 (t0) cc_final: 0.7669 (t0) REVERT: I 93 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8071 (mtm110) REVERT: J 1 MET cc_start: 0.7686 (pp-130) cc_final: 0.7201 (pp-130) REVERT: J 18 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7966 (mt-10) REVERT: J 102 VAL cc_start: 0.8865 (t) cc_final: 0.8659 (m) REVERT: J 147 ASP cc_start: 0.6925 (p0) cc_final: 0.6472 (t0) REVERT: K 320 ASP cc_start: 0.7279 (t0) cc_final: 0.6752 (t0) REVERT: M 42 LYS cc_start: 0.8604 (tttt) cc_final: 0.8108 (ptmt) REVERT: M 97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7957 (tt0) REVERT: N 106 THR cc_start: 0.8770 (p) cc_final: 0.8473 (p) REVERT: O 7 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8547 (mtpt) REVERT: P 18 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7795 (mt-10) REVERT: P 151 LYS cc_start: 0.8707 (mttp) cc_final: 0.8486 (mttp) REVERT: Q 130 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8572 (m110) REVERT: Q 234 MET cc_start: 0.7778 (tmm) cc_final: 0.7015 (tmm) outliers start: 98 outliers final: 81 residues processed: 413 average time/residue: 0.1656 time to fit residues: 108.4595 Evaluate side-chains 410 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 130 ASN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 117 SER Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 ASN Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [134, 150, 45, 326, 136, 68, 285, 224, 336, 82, 338] chunk 134 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 326 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 336 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.088865 restraints weight = 39041.272| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.60 r_work: 0.2864 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27186 Z= 0.114 Angle : 0.451 5.052 36846 Z= 0.243 Chirality : 0.044 0.165 4098 Planarity : 0.003 0.046 4770 Dihedral : 4.473 48.818 3744 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.68 % Allowed : 14.51 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3429 helix: 1.56 (0.26), residues: 393 sheet: -0.18 (0.15), residues: 1203 loop : -0.44 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 93 TYR 0.013 0.001 TYR K 207 PHE 0.016 0.001 PHE K 201 TRP 0.010 0.001 TRP E 265 HIS 0.002 0.000 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (27186) covalent geometry : angle 0.45116 / 0.24 (36846) hydrogen bonds : bond 0.02978 / 2.06 ( 489) hydrogen bonds : angle 4.91974 / 3.34 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 1.029 Fit side-chains REVERT: B 106 THR cc_start: 0.8771 (p) cc_final: 0.8538 (p) REVERT: C 7 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8479 (mtpt) REVERT: C 111 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: D 119 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7731 (ttmt) REVERT: E 174 ASN cc_start: 0.7642 (p0) cc_final: 0.7055 (t0) REVERT: E 234 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7311 (tmm) REVERT: G 42 LYS cc_start: 0.8443 (tttt) cc_final: 0.7969 (pttp) REVERT: G 147 ASP cc_start: 0.7857 (t0) cc_final: 0.7633 (t0) REVERT: I 93 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8100 (mtm110) REVERT: J 1 MET cc_start: 0.7715 (pp-130) cc_final: 0.7228 (pp-130) REVERT: K 234 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7387 (tmm) REVERT: M 26 VAL cc_start: 0.8773 (t) cc_final: 0.8571 (p) REVERT: M 42 LYS cc_start: 0.8587 (tttt) cc_final: 0.8099 (pttp) REVERT: M 97 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8072 (tt0) REVERT: N 106 THR cc_start: 0.8766 (p) cc_final: 0.8485 (p) REVERT: O 7 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8489 (mtpt) REVERT: P 1 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6835 (pp-130) REVERT: P 18 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7736 (mt-10) REVERT: P 119 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7613 (ttmt) REVERT: P 151 LYS cc_start: 0.8709 (mttp) cc_final: 0.8475 (mttp) REVERT: Q 130 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8413 (m-40) REVERT: Q 234 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7158 (tmm) outliers start: 76 outliers final: 58 residues processed: 401 average time/residue: 0.1681 time to fit residues: 106.0995 Evaluate side-chains 409 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 117 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 ASN Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 234 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [238, 32, 95, 90, 121, 159, 236, 292, 71, 127, 14] chunk 238 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 121 optimal weight: 0.0050 chunk 159 optimal weight: 0.9980 chunk 236 optimal weight: 0.5980 chunk 292 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN J 45 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN Q 130 ASN ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 347 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 = 0.3161 r_free = 0.3161 target = 0.102820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091080 restraints weight = 39010.325| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.58 r_work: 0.2897 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27186 Z= 0.077 Angle : 0.420 6.844 36846 Z= 0.226 Chirality : 0.044 0.230 4098 Planarity : 0.003 0.047 4770 Dihedral : 4.072 44.967 3744 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 15.47 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3429 helix: 1.80 (0.27), residues: 396 sheet: -0.01 (0.16), residues: 1179 loop : -0.34 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 93 TYR 0.012 0.001 TYR G 171 PHE 0.013 0.001 PHE K 201 TRP 0.007 0.001 TRP E 265 HIS 0.001 0.000 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (27186) covalent geometry : angle 0.42020 / 0.23 (36846) hydrogen bonds : bond 0.02466 / 1.72 ( 489) hydrogen bonds : angle 4.72490 / 3.18 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 0.940 Fit side-chains REVERT: A 97 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8050 (tt0) REVERT: B 106 THR cc_start: 0.8750 (p) cc_final: 0.8530 (p) REVERT: C 7 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8384 (mtpt) REVERT: D 119 LYS cc_start: 0.8044 (tmtt) cc_final: 0.7752 (ttmt) REVERT: E 89 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: E 174 ASN cc_start: 0.7524 (p0) cc_final: 0.6949 (t0) REVERT: E 234 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: F 763 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7611 (ttm-80) REVERT: G 42 LYS cc_start: 0.8437 (tttt) cc_final: 0.7970 (pttp) REVERT: H 42 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8245 (mmtt) REVERT: I 93 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8103 (mtm110) REVERT: J 1 MET cc_start: 0.7668 (pp-130) cc_final: 0.7202 (pp-130) REVERT: J 147 ASP cc_start: 0.6714 (t0) cc_final: 0.6161 (t0) REVERT: M 42 LYS cc_start: 0.8531 (tttt) cc_final: 0.8055 (pttp) REVERT: M 97 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8091 (tt0) REVERT: N 106 THR cc_start: 0.8778 (p) cc_final: 0.8515 (p) REVERT: O 7 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8426 (mtpt) REVERT: P 1 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6918 (pp-130) REVERT: P 18 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7653 (mt-10) REVERT: P 55 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8173 (mm-30) REVERT: P 119 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7678 (ttmm) REVERT: P 151 LYS cc_start: 0.8698 (mttp) cc_final: 0.8472 (mttp) REVERT: P 169 MET cc_start: 0.8665 (ttm) cc_final: 0.8149 (ttm) REVERT: Q 130 ASN cc_start: 0.8573 (m-40) cc_final: 0.8230 (m-40) REVERT: Q 234 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7129 (tmm) REVERT: R 763 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7489 (mtm-85) outliers start: 56 outliers final: 43 residues processed: 390 average time/residue: 0.1726 time to fit residues: 105.3526 Evaluate side-chains 378 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain Q residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [267, 260, 209, 69, 174, 193, 201, 251, 169, 37, 289] chunk 267 optimal weight: 0.2980 chunk 260 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 193 optimal weight: 0.0970 chunk 201 optimal weight: 5.9990 chunk 251 optimal weight: 0.2980 chunk 169 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.089962 restraints weight = 39087.840| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.59 r_work: 0.2884 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27186 Z= 0.102 Angle : 0.436 5.377 36846 Z= 0.234 Chirality : 0.044 0.205 4098 Planarity : 0.003 0.047 4770 Dihedral : 4.107 46.446 3744 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.08 % Allowed : 15.50 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3429 helix: 1.77 (0.27), residues: 396 sheet: 0.01 (0.16), residues: 1176 loop : -0.31 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 93 TYR 0.011 0.001 TYR K 207 PHE 0.017 0.001 PHE Q 201 TRP 0.008 0.001 TRP D 15 HIS 0.001 0.000 HIS M 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (27186) covalent geometry : angle 0.43603 / 0.23 (36846) hydrogen bonds : bond 0.02726 / 1.90 ( 489) hydrogen bonds : angle 4.73261 / 3.20 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 1.004 Fit side-chains REVERT: A 97 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8044 (tt0) REVERT: B 106 THR cc_start: 0.8804 (p) cc_final: 0.8568 (p) REVERT: C 7 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8398 (mtpt) REVERT: D 119 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7750 (ttmt) REVERT: E 130 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8242 (m-40) REVERT: E 174 ASN cc_start: 0.7542 (p0) cc_final: 0.6942 (t0) REVERT: E 234 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: G 42 LYS cc_start: 0.8429 (tttt) cc_final: 0.7969 (pttp) REVERT: I 93 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8104 (mtm110) REVERT: J 1 MET cc_start: 0.7619 (pp-130) cc_final: 0.7205 (pp-130) REVERT: J 147 ASP cc_start: 0.6729 (t0) cc_final: 0.6182 (t0) REVERT: K 234 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: M 42 LYS cc_start: 0.8531 (tttt) cc_final: 0.8065 (pttp) REVERT: M 97 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8097 (tt0) REVERT: N 42 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8286 (mttt) REVERT: N 106 THR cc_start: 0.8771 (p) cc_final: 0.8504 (p) REVERT: O 7 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8434 (mtpt) REVERT: P 1 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7013 (pp-130) REVERT: P 18 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7686 (mt-10) REVERT: P 119 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7629 (ttmm) REVERT: P 151 LYS cc_start: 0.8725 (mttp) cc_final: 0.8467 (mttp) REVERT: P 169 MET cc_start: 0.8692 (ttm) cc_final: 0.8184 (ttm) REVERT: Q 89 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: Q 130 ASN cc_start: 0.8485 (m-40) cc_final: 0.8220 (m-40) REVERT: Q 234 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7174 (tmm) REVERT: R 763 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7448 (mtm-85) outliers start: 59 outliers final: 49 residues processed: 374 average time/residue: 0.1771 time to fit residues: 103.9954 Evaluate side-chains 390 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain Q residue 234 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [9, 210, 34, 13, 18, 44, 180, 50, 171, 257, 19] chunk 9 optimal weight: 0.1980 chunk 210 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 130 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.091613 restraints weight = 39206.475| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.59 r_work: 0.2901 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27186 Z= 0.081 Angle : 0.418 6.028 36846 Z= 0.224 Chirality : 0.043 0.178 4098 Planarity : 0.003 0.048 4770 Dihedral : 3.925 44.675 3744 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.01 % Allowed : 15.78 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3429 helix: 1.88 (0.27), residues: 396 sheet: 0.08 (0.16), residues: 1173 loop : -0.25 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 93 TYR 0.010 0.001 TYR K 207 PHE 0.023 0.001 PHE K 201 TRP 0.007 0.001 TRP K 265 HIS 0.001 0.000 HIS M 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 (27186) covalent geometry : angle 0.41779 / 0.22 (36846) hydrogen bonds : bond 0.02467 / 1.73 ( 489) hydrogen bonds : angle 4.66637 / 3.15 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 0.923 Fit side-chains REVERT: A 42 LYS cc_start: 0.8688 (tptt) cc_final: 0.8155 (pttp) REVERT: A 97 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8075 (tt0) REVERT: B 106 THR cc_start: 0.8775 (p) cc_final: 0.8545 (p) REVERT: C 7 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8365 (mtpt) REVERT: D 119 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7753 (ttmt) REVERT: E 89 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: E 130 ASN cc_start: 0.8584 (m-40) cc_final: 0.8155 (m-40) REVERT: E 174 ASN cc_start: 0.7531 (p0) cc_final: 0.6937 (t0) REVERT: E 234 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: G 42 LYS cc_start: 0.8408 (tttt) cc_final: 0.7951 (pttp) REVERT: I 93 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8111 (mtm110) REVERT: J 1 MET cc_start: 0.7575 (pp-130) cc_final: 0.7159 (pp-130) REVERT: K 234 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7287 (tmm) REVERT: M 42 LYS cc_start: 0.8494 (tttt) cc_final: 0.8029 (pttp) REVERT: M 97 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8106 (tt0) REVERT: N 106 THR cc_start: 0.8758 (p) cc_final: 0.8496 (p) REVERT: O 7 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8382 (mtpt) REVERT: P 1 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7211 (pp-130) REVERT: P 18 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7661 (mt-10) REVERT: P 119 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7701 (ttmm) REVERT: P 151 LYS cc_start: 0.8723 (mttp) cc_final: 0.8459 (mttp) REVERT: P 169 MET cc_start: 0.8636 (ttm) cc_final: 0.8099 (ttm) REVERT: Q 89 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: Q 130 ASN cc_start: 0.8458 (m-40) cc_final: 0.8184 (m-40) REVERT: Q 234 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7118 (tmm) REVERT: R 763 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7437 (mtm-85) outliers start: 57 outliers final: 48 residues processed: 376 average time/residue: 0.1713 time to fit residues: 101.3545 Evaluate side-chains 386 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain Q residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [36, 160, 176, 27, 313, 248, 100, 320, 16, 131, 108] chunk 36 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 320 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.087247 restraints weight = 39405.811| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.61 r_work: 0.2839 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27186 Z= 0.201 Angle : 0.512 5.585 36846 Z= 0.275 Chirality : 0.047 0.199 4098 Planarity : 0.004 0.046 4770 Dihedral : 4.637 54.053 3744 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.26 % Allowed : 15.40 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3429 helix: 1.41 (0.26), residues: 396 sheet: 0.04 (0.16), residues: 1137 loop : -0.40 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 93 TYR 0.017 0.002 TYR M 200 PHE 0.026 0.002 PHE K 201 TRP 0.011 0.001 TRP D 15 HIS 0.003 0.001 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (27186) covalent geometry : angle 0.51159 / 0.27 (36846) hydrogen bonds : bond 0.03588 / 2.48 ( 489) hydrogen bonds : angle 4.97553 / 3.39 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6858 Ramachandran restraints generated. 3429 Oldfield, 0 Emsley, 3429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 1.008 Fit side-chains REVERT: B 106 THR cc_start: 0.8828 (p) cc_final: 0.8559 (p) REVERT: B 180 GLU cc_start: 0.8510 (pt0) cc_final: 0.8291 (pt0) REVERT: C 7 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8536 (mtpt) REVERT: E 89 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: E 174 ASN cc_start: 0.7699 (p0) cc_final: 0.7087 (t0) REVERT: E 234 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7362 (tmm) REVERT: G 42 LYS cc_start: 0.8457 (tttt) cc_final: 0.8017 (pttp) REVERT: I 93 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8096 (mtm110) REVERT: J 1 MET cc_start: 0.7656 (pp-130) cc_final: 0.7206 (pp-130) REVERT: J 147 ASP cc_start: 0.6706 (t0) cc_final: 0.6136 (t0) REVERT: M 42 LYS cc_start: 0.8564 (tttt) cc_final: 0.8088 (pttp) REVERT: M 97 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8083 (tt0) REVERT: N 106 THR cc_start: 0.8791 (p) cc_final: 0.8498 (p) REVERT: O 7 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8521 (mtpt) REVERT: P 18 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7797 (mt-10) REVERT: P 151 LYS cc_start: 0.8728 (mttp) cc_final: 0.8472 (mttp) REVERT: Q 40 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7703 (mt-10) REVERT: Q 234 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7001 (tmm) outliers start: 64 outliers final: 57 residues processed: 363 average time/residue: 0.1672 time to fit residues: 96.0550 Evaluate side-chains 381 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 117 SER Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 145 SER Chi-restraints excluded: chain Q residue 167 ILE Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain Q residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: [307, 253, 239, 259, 12, 156, 133, 182, 35, 287, 99] chunk 307 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 chunk 239 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN D 45 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 45 GLN ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088101 restraints weight = 39292.632| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.58 r_work: 0.2854 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27186 Z= 0.148 Angle : 0.473 6.236 36846 Z= 0.254 Chirality : 0.045 0.189 4098 Planarity : 0.003 0.047 4770 Dihedral : 4.498 51.799 3744 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.22 % Allowed : 15.64 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3429 helix: 1.47 (0.26), residues: 396 sheet: -0.09 (0.15), residues: 1182 loop : -0.32 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 93 TYR 0.014 0.001 TYR K 207 PHE 0.024 0.001 PHE K 201 TRP 0.010 0.001 TRP K 76 HIS 0.003 0.001 HIS O 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (27186) covalent geometry : angle 0.47320 / 0.25 (36846) hydrogen bonds : bond 0.03174 / 2.20 ( 489) hydrogen bonds : angle 4.91520 / 3.34 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6117.58 seconds wall clock time: 105 minutes 41.26 seconds (6341.26 seconds total)