Starting phenix.real_space_refine on Thu Mar 5 20:19:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pv2_13664/03_2026/7pv2_13664.map" } resolution = 3.2 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= 0.004 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 108 5.16 5 C 16476 2.51 5 N 4176 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "E" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "F" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "H" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "I" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "J" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "K" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "L" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 5.26, per 1000 atoms: 0.21 Number of scatterers: 25440 At special positions: 0 Unit cell: (167.99, 167.99, 88.81, 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 108 16.00 O 4680 8.00 N 4176 7.00 C 16476 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: 1.88 Conformation dependent library (CDL) restraints added in 801.1 milliseconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 42.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 Proline residue: A 262 - end of helix Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 274 Proline residue: B 262 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.630A pdb=" N ILE C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 274 Proline residue: C 262 - end of helix Processing helix chain 'D' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 274 Proline residue: D 262 - end of helix Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR E 177 " --> pdb=" O MET E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 274 Proline residue: E 262 - end of helix Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR F 177 " --> pdb=" O MET F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 274 Proline residue: F 262 - end of helix Processing helix chain 'G' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG G 16 " --> pdb=" O GLY G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR G 177 " --> pdb=" O MET G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 274 Proline residue: G 262 - end of helix Processing helix chain 'H' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE H 14 " --> pdb=" O THR H 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU H 138 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR H 177 " --> pdb=" O MET H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 274 Proline residue: H 262 - end of helix Processing helix chain 'I' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE I 14 " --> pdb=" O THR I 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG I 16 " --> pdb=" O GLY I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET I 173 " --> pdb=" O ASP I 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR I 177 " --> pdb=" O MET I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE I 216 " --> pdb=" O LEU I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 274 Proline residue: I 262 - end of helix Processing helix chain 'J' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE J 14 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 16 " --> pdb=" O GLY J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 36 removed outlier: 3.847A pdb=" N ARG J 24 " --> pdb=" O ASN J 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 141 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET J 173 " --> pdb=" O ASP J 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR J 177 " --> pdb=" O MET J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE J 216 " --> pdb=" O LEU J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 274 Proline residue: J 262 - end of helix Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE K 14 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET K 141 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET K 173 " --> pdb=" O ASP K 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR K 177 " --> pdb=" O MET K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE K 216 " --> pdb=" O LEU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 274 Proline residue: K 262 - end of helix Processing helix chain 'L' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE L 14 " --> pdb=" O THR L 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG L 24 " --> pdb=" O ASN L 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET L 141 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET L 173 " --> pdb=" O ASP L 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE L 216 " --> pdb=" O LEU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 274 Proline residue: L 262 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS A 281 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 279 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL A 161 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE B 188 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 163 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.150A pdb=" N VAL A 186 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS B 281 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 279 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL B 161 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE C 188 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 163 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS C 281 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 279 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 202 removed outlier: 7.170A pdb=" N VAL C 161 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE D 188 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 163 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS D 281 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 279 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB8, first strand: chain 'D' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL D 161 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE E 188 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 163 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS E 281 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 279 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC3, first strand: chain 'E' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL E 161 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE F 188 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 163 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS F 281 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER F 279 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC6, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'F' and resid 199 through 202 removed outlier: 7.248A pdb=" N VAL F 161 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE G 188 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 163 " --> pdb=" O PHE G 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS G 281 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER G 279 " --> pdb=" O GLN G 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AD2, first strand: chain 'G' and resid 199 through 202 removed outlier: 4.220A pdb=" N VAL H 186 " --> pdb=" O VAL G 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS H 281 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 279 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AD6, first strand: chain 'H' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL H 161 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE I 188 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 163 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS I 281 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER I 279 " --> pdb=" O GLN I 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'I' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL I 161 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE J 188 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE I 163 " --> pdb=" O PHE J 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS J 281 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 279 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AE4, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AE5, first strand: chain 'J' and resid 199 through 202 removed outlier: 7.172A pdb=" N VAL J 161 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE K 188 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE J 163 " --> pdb=" O PHE K 188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS K 281 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 279 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AE9, first strand: chain 'K' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL K 161 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE L 188 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE K 163 " --> pdb=" O PHE L 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS L 281 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 279 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AF3, first strand: chain 'L' and resid 91 through 93 966 hydrogen bonds defined for protein. 2826 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: 3.99 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8053 1.34 - 1.46: 6031 1.46 - 1.57: 11764 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 26052 Sorted by residual: bond pdb=" CB ILE A 150 " pdb=" CG2 ILE A 150 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB ILE D 150 " pdb=" CG2 ILE D 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB ILE E 150 " pdb=" CG2 ILE E 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE B 150 " pdb=" CG2 ILE B 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE H 150 " pdb=" CG2 ILE H 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 26047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33302 1.40 - 2.81: 1614 2.81 - 4.21: 259 4.21 - 5.62: 45 5.62 - 7.02: 12 Bond angle restraints: 35232 Sorted by residual: angle pdb=" CA GLY E 190 " pdb=" C GLY E 190 " pdb=" O GLY E 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY H 190 " pdb=" C GLY H 190 " pdb=" O GLY H 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY D 190 " pdb=" C GLY D 190 " pdb=" O GLY D 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.79e+00 angle pdb=" CA GLY B 190 " pdb=" C GLY B 190 " pdb=" O GLY B 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.75e+00 angle pdb=" CA GLY J 190 " pdb=" C GLY J 190 " pdb=" O GLY J 190 " ideal model delta sigma weight residual 122.37 120.48 1.89 7.30e-01 1.88e+00 6.73e+00 ... (remaining 35227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 13368 15.55 - 31.09: 1692 31.09 - 46.64: 223 46.64 - 62.19: 101 62.19 - 77.74: 84 Dihedral angle restraints: 15468 sinusoidal: 6396 harmonic: 9072 Sorted by residual: dihedral pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N GLY L 74 " pdb=" CA GLY L 74 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU F 73 " pdb=" C LEU F 73 " pdb=" N GLY F 74 " pdb=" CA GLY F 74 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU I 73 " pdb=" C LEU I 73 " pdb=" N GLY I 74 " pdb=" CA GLY I 74 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3090 0.086 - 0.171: 383 0.171 - 0.257: 108 0.257 - 0.343: 79 0.343 - 0.428: 24 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CB ILE A 135 " pdb=" CA ILE A 135 " pdb=" CG1 ILE A 135 " pdb=" CG2 ILE A 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE K 135 " pdb=" CA ILE K 135 " pdb=" CG1 ILE K 135 " pdb=" CG2 ILE K 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE E 135 " pdb=" CA ILE E 135 " pdb=" CG1 ILE E 135 " pdb=" CG2 ILE E 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 3681 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN J 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN J 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN J 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN A 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 251 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" CD GLN H 251 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN H 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN H 251 " -0.014 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 205 2.56 - 3.14: 20668 3.14 - 3.73: 35405 3.73 - 4.31: 51075 4.31 - 4.90: 88641 Nonbonded interactions: 195994 Sorted by model distance: nonbonded pdb=" OD1 ASP J 169 " pdb=" OG SER J 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG SER B 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP K 169 " pdb=" OG SER K 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP D 169 " pdb=" OG SER D 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP F 169 " pdb=" OG SER F 172 " model vdw 1.971 3.040 ... (remaining 195989 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=0.98 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: 1.970 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.070 26052 Z= 0.443 Angle : 0.714 7.019 35232 Z= 0.392 Chirality : 0.084 0.428 3684 Planarity : 0.004 0.039 4536 Dihedral : 14.851 77.735 9708 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.84 (0.12), residues: 3036 helix: -1.58 (0.13), residues: 1272 sheet: -3.39 (0.35), residues: 144 loop : -3.41 (0.11), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 16 TYR 0.012 0.002 TYR L 273 PHE 0.011 0.002 PHE L 64 TRP 0.010 0.002 TRP J 22 HIS 0.001 0.000 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.01086 (26052) covalent geometry : angle 0.71365 (35232) hydrogen bonds : bond 0.20041 ( 966) hydrogen bonds : angle 6.72189 ( 2826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8329 (pptt) cc_final: 0.7836 (pptt) REVERT: E 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.7783 (pptt) REVERT: E 155 ASN cc_start: 0.8270 (t0) cc_final: 0.8022 (t0) REVERT: H 45 LYS cc_start: 0.8037 (pptt) cc_final: 0.7702 (pptt) REVERT: H 207 TYR cc_start: 0.8691 (t80) cc_final: 0.7627 (t80) REVERT: J 69 MET cc_start: 0.7164 (ttt) cc_final: 0.6883 (tmm) REVERT: K 45 LYS cc_start: 0.8273 (pptt) cc_final: 0.8016 (pptt) REVERT: K 207 TYR cc_start: 0.8807 (t80) cc_final: 0.7950 (t80) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.1846 time to fit residues: 137.9939 Evaluate side-chains 380 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 271 ASN B 36 GLN B 155 ASN B 271 ASN C 36 GLN D 36 GLN D 271 ASN E 36 GLN E 271 ASN F 36 GLN F 271 ASN G 36 GLN G 58 GLN G 155 ASN G 271 ASN H 36 GLN H 271 ASN I 36 GLN I 271 ASN J 36 GLN J 271 ASN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN L 36 GLN L 271 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121620 restraints weight = 33902.511| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 26052 Z= 0.111 Angle : 0.521 6.819 35232 Z= 0.269 Chirality : 0.044 0.141 3684 Planarity : 0.003 0.034 4536 Dihedral : 3.864 18.299 3432 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.44 % Allowed : 6.70 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.14), residues: 3036 helix: -0.18 (0.15), residues: 1284 sheet: -2.96 (0.36), residues: 144 loop : -2.40 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.015 0.001 TYR G 92 PHE 0.009 0.001 PHE D 216 TRP 0.013 0.001 TRP C 40 HIS 0.001 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00253 (26052) covalent geometry : angle 0.52065 (35232) hydrogen bonds : bond 0.03923 ( 966) hydrogen bonds : angle 4.75696 ( 2826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 438 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8301 (pptt) cc_final: 0.7607 (pttp) REVERT: A 110 MET cc_start: 0.7308 (ptm) cc_final: 0.6877 (ptm) REVERT: B 45 LYS cc_start: 0.8286 (pptt) cc_final: 0.7711 (pptt) REVERT: C 45 LYS cc_start: 0.8475 (pptt) cc_final: 0.8025 (pttp) REVERT: C 85 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7572 (mm) REVERT: D 45 LYS cc_start: 0.8244 (pptt) cc_final: 0.7662 (pttp) REVERT: E 24 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7899 (mtp180) REVERT: E 45 LYS cc_start: 0.8246 (pptt) cc_final: 0.7921 (pttp) REVERT: F 45 LYS cc_start: 0.8288 (pptt) cc_final: 0.7818 (pttp) REVERT: H 24 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7937 (mtp180) REVERT: H 73 LEU cc_start: 0.7897 (tp) cc_final: 0.7547 (tt) REVERT: I 24 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7962 (mtp180) REVERT: J 45 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7743 (pttp) REVERT: K 45 LYS cc_start: 0.8262 (pptt) cc_final: 0.7820 (pptt) REVERT: L 24 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7999 (mtp180) REVERT: L 85 LEU cc_start: 0.8123 (tp) cc_final: 0.7795 (mm) outliers start: 12 outliers final: 3 residues processed: 443 average time/residue: 0.1971 time to fit residues: 129.2911 Evaluate side-chains 387 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 382 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 265 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111962 restraints weight = 34613.706| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.25 r_work: 0.3158 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26052 Z= 0.173 Angle : 0.540 4.742 35232 Z= 0.286 Chirality : 0.046 0.154 3684 Planarity : 0.003 0.030 4536 Dihedral : 4.001 18.854 3432 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.07 % Allowed : 8.85 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.14), residues: 3036 helix: 0.21 (0.15), residues: 1284 sheet: -2.81 (0.36), residues: 144 loop : -1.97 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 24 TYR 0.013 0.001 TYR G 92 PHE 0.016 0.002 PHE L 64 TRP 0.007 0.001 TRP L 40 HIS 0.002 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00421 (26052) covalent geometry : angle 0.53990 (35232) hydrogen bonds : bond 0.04930 ( 966) hydrogen bonds : angle 4.79777 ( 2826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 403 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8417 (pptt) cc_final: 0.7902 (pttp) REVERT: A 110 MET cc_start: 0.7539 (ptm) cc_final: 0.7154 (ptm) REVERT: B 45 LYS cc_start: 0.8397 (pptt) cc_final: 0.7729 (pptt) REVERT: B 85 LEU cc_start: 0.8151 (tp) cc_final: 0.7832 (mm) REVERT: B 101 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6952 (tttt) REVERT: B 114 LEU cc_start: 0.2263 (OUTLIER) cc_final: 0.1391 (pp) REVERT: C 85 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7950 (mm) REVERT: C 114 LEU cc_start: 0.2808 (OUTLIER) cc_final: 0.2132 (pp) REVERT: D 45 LYS cc_start: 0.8428 (pptt) cc_final: 0.7887 (pttp) REVERT: D 109 ASP cc_start: 0.7334 (t0) cc_final: 0.6817 (t0) REVERT: E 24 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8104 (mtm110) REVERT: E 45 LYS cc_start: 0.8288 (pptt) cc_final: 0.7715 (pptt) REVERT: E 85 LEU cc_start: 0.8102 (tp) cc_final: 0.7751 (mm) REVERT: E 114 LEU cc_start: 0.2128 (OUTLIER) cc_final: 0.1300 (pp) REVERT: E 224 MET cc_start: 0.8843 (mmp) cc_final: 0.8592 (mmp) REVERT: F 114 LEU cc_start: 0.2415 (OUTLIER) cc_final: 0.1418 (pp) REVERT: F 141 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8442 (ptt) REVERT: G 92 TYR cc_start: 0.8062 (t80) cc_final: 0.7761 (t80) REVERT: G 197 ASP cc_start: 0.7807 (p0) cc_final: 0.7557 (p0) REVERT: H 24 ARG cc_start: 0.8436 (mtp180) cc_final: 0.8070 (mtm110) REVERT: H 85 LEU cc_start: 0.8150 (tp) cc_final: 0.7764 (mm) REVERT: H 114 LEU cc_start: 0.2443 (OUTLIER) cc_final: 0.1578 (pp) REVERT: I 24 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8197 (mtm110) REVERT: I 114 LEU cc_start: 0.2639 (OUTLIER) cc_final: 0.1987 (pp) REVERT: J 45 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7884 (pttp) REVERT: K 45 LYS cc_start: 0.8405 (pptt) cc_final: 0.7999 (pttp) REVERT: K 85 LEU cc_start: 0.8204 (tp) cc_final: 0.7876 (mm) REVERT: K 101 LYS cc_start: 0.7280 (ttmt) cc_final: 0.7078 (tttt) REVERT: K 114 LEU cc_start: 0.2724 (OUTLIER) cc_final: 0.1795 (pp) REVERT: L 24 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8198 (mtm110) REVERT: L 85 LEU cc_start: 0.8289 (tp) cc_final: 0.8076 (mm) REVERT: L 114 LEU cc_start: 0.2859 (OUTLIER) cc_final: 0.1929 (pp) REVERT: L 181 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8298 (tt0) outliers start: 29 outliers final: 6 residues processed: 421 average time/residue: 0.1985 time to fit residues: 125.2324 Evaluate side-chains 384 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 366 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 68 optimal weight: 0.0570 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114173 restraints weight = 34415.732| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.23 r_work: 0.3134 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26052 Z= 0.114 Angle : 0.477 6.691 35232 Z= 0.250 Chirality : 0.043 0.150 3684 Planarity : 0.003 0.027 4536 Dihedral : 3.873 18.182 3432 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.15 % Allowed : 10.00 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.15), residues: 3036 helix: 0.50 (0.15), residues: 1296 sheet: -2.69 (0.37), residues: 144 loop : -1.58 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.012 0.001 TYR J 8 PHE 0.011 0.001 PHE L 64 TRP 0.007 0.001 TRP E 22 HIS 0.002 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00273 (26052) covalent geometry : angle 0.47707 (35232) hydrogen bonds : bond 0.03807 ( 966) hydrogen bonds : angle 4.46807 ( 2826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 397 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8336 (pptt) cc_final: 0.7806 (pttp) REVERT: B 85 LEU cc_start: 0.8164 (tp) cc_final: 0.7847 (mm) REVERT: B 114 LEU cc_start: 0.2209 (OUTLIER) cc_final: 0.1594 (pp) REVERT: C 109 ASP cc_start: 0.7047 (t0) cc_final: 0.6803 (t0) REVERT: C 114 LEU cc_start: 0.2604 (OUTLIER) cc_final: 0.2051 (pp) REVERT: D 45 LYS cc_start: 0.8387 (pptt) cc_final: 0.7882 (pttp) REVERT: E 24 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7998 (mtp-110) REVERT: E 85 LEU cc_start: 0.8132 (tp) cc_final: 0.7818 (mm) REVERT: E 114 LEU cc_start: 0.2073 (OUTLIER) cc_final: 0.1285 (pp) REVERT: F 114 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.1873 (pp) REVERT: H 24 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7965 (mtp-110) REVERT: H 85 LEU cc_start: 0.8089 (tp) cc_final: 0.7704 (mm) REVERT: H 114 LEU cc_start: 0.2479 (OUTLIER) cc_final: 0.1697 (pp) REVERT: I 24 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8047 (mtp-110) REVERT: I 109 ASP cc_start: 0.7072 (t0) cc_final: 0.6810 (t0) REVERT: I 114 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.1789 (pp) REVERT: J 45 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7692 (pttp) REVERT: K 39 GLU cc_start: 0.8205 (tt0) cc_final: 0.7869 (tt0) REVERT: K 45 LYS cc_start: 0.8339 (pptt) cc_final: 0.7941 (pttp) REVERT: K 85 LEU cc_start: 0.8200 (tp) cc_final: 0.7900 (mm) REVERT: K 114 LEU cc_start: 0.2496 (OUTLIER) cc_final: 0.1679 (pp) REVERT: L 24 ARG cc_start: 0.8343 (mtp180) cc_final: 0.8039 (mtp-110) REVERT: L 85 LEU cc_start: 0.8251 (tp) cc_final: 0.8045 (mm) REVERT: L 114 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.1917 (pp) REVERT: L 181 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8252 (tt0) outliers start: 31 outliers final: 5 residues processed: 418 average time/residue: 0.1940 time to fit residues: 121.4899 Evaluate side-chains 389 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 374 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 297 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 82 GLN K 36 GLN K 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110484 restraints weight = 34360.523| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.19 r_work: 0.3134 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26052 Z= 0.180 Angle : 0.533 7.416 35232 Z= 0.281 Chirality : 0.045 0.140 3684 Planarity : 0.003 0.026 4536 Dihedral : 4.045 17.782 3432 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.04 % Allowed : 11.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.15), residues: 3036 helix: 0.60 (0.15), residues: 1296 sheet: -2.66 (0.39), residues: 144 loop : -1.44 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 59 TYR 0.028 0.001 TYR G 92 PHE 0.016 0.001 PHE C 64 TRP 0.008 0.002 TRP B 22 HIS 0.001 0.000 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00443 (26052) covalent geometry : angle 0.53348 (35232) hydrogen bonds : bond 0.04751 ( 966) hydrogen bonds : angle 4.61431 ( 2826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 396 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8413 (pptt) cc_final: 0.7898 (pttp) REVERT: B 39 GLU cc_start: 0.8263 (tt0) cc_final: 0.7984 (tt0) REVERT: B 45 LYS cc_start: 0.8429 (pptt) cc_final: 0.7761 (pptt) REVERT: B 85 LEU cc_start: 0.8328 (tp) cc_final: 0.8061 (mm) REVERT: B 114 LEU cc_start: 0.2492 (OUTLIER) cc_final: 0.1674 (pp) REVERT: B 224 MET cc_start: 0.8883 (mmp) cc_final: 0.8673 (mmp) REVERT: C 114 LEU cc_start: 0.2639 (OUTLIER) cc_final: 0.2030 (pp) REVERT: D 45 LYS cc_start: 0.8441 (pptt) cc_final: 0.8236 (pttp) REVERT: E 24 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8131 (mtm110) REVERT: E 85 LEU cc_start: 0.8275 (tp) cc_final: 0.7993 (mm) REVERT: E 114 LEU cc_start: 0.2275 (OUTLIER) cc_final: 0.1491 (pp) REVERT: F 114 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.1985 (pp) REVERT: G 70 TYR cc_start: 0.6826 (m-80) cc_final: 0.6481 (m-80) REVERT: H 24 ARG cc_start: 0.8446 (mtp180) cc_final: 0.8169 (mtp-110) REVERT: H 39 GLU cc_start: 0.8196 (tt0) cc_final: 0.7891 (tt0) REVERT: H 45 LYS cc_start: 0.8396 (pptt) cc_final: 0.7740 (pptt) REVERT: H 85 LEU cc_start: 0.8218 (tp) cc_final: 0.7886 (mm) REVERT: H 114 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.1828 (pp) REVERT: I 24 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8211 (mtm110) REVERT: I 114 LEU cc_start: 0.3011 (OUTLIER) cc_final: 0.2059 (pp) REVERT: K 39 GLU cc_start: 0.8236 (tt0) cc_final: 0.7954 (tt0) REVERT: K 45 LYS cc_start: 0.8415 (pptt) cc_final: 0.7751 (pptt) REVERT: K 114 LEU cc_start: 0.2711 (OUTLIER) cc_final: 0.1850 (pp) REVERT: L 24 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8205 (mtm110) REVERT: L 114 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2057 (pp) REVERT: L 181 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8312 (tt0) outliers start: 28 outliers final: 8 residues processed: 416 average time/residue: 0.1969 time to fit residues: 120.5064 Evaluate side-chains 338 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 321 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114232 restraints weight = 34500.502| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.19 r_work: 0.3203 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26052 Z= 0.099 Angle : 0.469 7.189 35232 Z= 0.246 Chirality : 0.042 0.163 3684 Planarity : 0.003 0.027 4536 Dihedral : 3.867 18.432 3432 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.15 % Allowed : 12.19 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.15), residues: 3036 helix: 0.92 (0.15), residues: 1296 sheet: -2.63 (0.39), residues: 144 loop : -1.26 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.013 0.001 TYR I 8 PHE 0.010 0.001 PHE F 64 TRP 0.007 0.001 TRP H 22 HIS 0.001 0.000 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00230 (26052) covalent geometry : angle 0.46854 (35232) hydrogen bonds : bond 0.03493 ( 966) hydrogen bonds : angle 4.29750 ( 2826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8444 (pptt) cc_final: 0.7871 (pttp) REVERT: A 85 LEU cc_start: 0.8421 (tp) cc_final: 0.7916 (mm) REVERT: B 39 GLU cc_start: 0.8206 (tt0) cc_final: 0.7877 (tt0) REVERT: B 45 LYS cc_start: 0.8369 (pptt) cc_final: 0.7963 (pttp) REVERT: B 85 LEU cc_start: 0.8308 (tp) cc_final: 0.8036 (mm) REVERT: B 114 LEU cc_start: 0.2525 (OUTLIER) cc_final: 0.1753 (pp) REVERT: C 114 LEU cc_start: 0.2834 (OUTLIER) cc_final: 0.2102 (pp) REVERT: D 45 LYS cc_start: 0.8457 (pptt) cc_final: 0.7962 (pttp) REVERT: E 24 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8226 (mtp-110) REVERT: E 85 LEU cc_start: 0.8286 (tp) cc_final: 0.8016 (mm) REVERT: E 114 LEU cc_start: 0.2220 (OUTLIER) cc_final: 0.1515 (pp) REVERT: F 114 LEU cc_start: 0.2743 (OUTLIER) cc_final: 0.2022 (pp) REVERT: H 24 ARG cc_start: 0.8420 (mtp180) cc_final: 0.8172 (mtp-110) REVERT: H 39 GLU cc_start: 0.8183 (tt0) cc_final: 0.7872 (tt0) REVERT: H 85 LEU cc_start: 0.8229 (tp) cc_final: 0.7912 (mm) REVERT: H 114 LEU cc_start: 0.2593 (OUTLIER) cc_final: 0.1848 (pp) REVERT: I 14 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8872 (mm) REVERT: I 24 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8166 (mtm110) REVERT: I 114 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2170 (pp) REVERT: I 141 MET cc_start: 0.8715 (ptt) cc_final: 0.8426 (ptt) REVERT: J 45 LYS cc_start: 0.8652 (pttp) cc_final: 0.8407 (pttp) REVERT: J 85 LEU cc_start: 0.8485 (tp) cc_final: 0.8012 (mm) REVERT: K 39 GLU cc_start: 0.8187 (tt0) cc_final: 0.7890 (tt0) REVERT: K 45 LYS cc_start: 0.8358 (pptt) cc_final: 0.7992 (pttp) REVERT: K 114 LEU cc_start: 0.2624 (OUTLIER) cc_final: 0.1726 (pp) REVERT: L 24 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8175 (mtm110) REVERT: L 114 LEU cc_start: 0.2787 (OUTLIER) cc_final: 0.2053 (pp) REVERT: L 141 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8226 (ptt) outliers start: 31 outliers final: 12 residues processed: 373 average time/residue: 0.2045 time to fit residues: 110.5895 Evaluate side-chains 359 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 337 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 192 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN K 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106826 restraints weight = 34261.894| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.27 r_work: 0.3095 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 26052 Z= 0.235 Angle : 0.572 5.731 35232 Z= 0.300 Chirality : 0.047 0.163 3684 Planarity : 0.003 0.025 4536 Dihedral : 4.193 18.006 3432 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.30 % Allowed : 12.67 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.15), residues: 3036 helix: 0.80 (0.15), residues: 1284 sheet: -2.60 (0.40), residues: 144 loop : -1.30 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.013 0.002 TYR I 72 PHE 0.019 0.002 PHE E 64 TRP 0.010 0.002 TRP B 22 HIS 0.002 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00583 (26052) covalent geometry : angle 0.57217 (35232) hydrogen bonds : bond 0.05233 ( 966) hydrogen bonds : angle 4.69214 ( 2826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 335 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8423 (pptt) cc_final: 0.7928 (pttp) REVERT: A 85 LEU cc_start: 0.8529 (tp) cc_final: 0.8083 (mm) REVERT: B 39 GLU cc_start: 0.8357 (tt0) cc_final: 0.8054 (tt0) REVERT: B 45 LYS cc_start: 0.8407 (pptt) cc_final: 0.7755 (pptt) REVERT: B 85 LEU cc_start: 0.8308 (tp) cc_final: 0.7976 (mm) REVERT: B 114 LEU cc_start: 0.2598 (OUTLIER) cc_final: 0.1763 (pp) REVERT: C 114 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2049 (pp) REVERT: D 45 LYS cc_start: 0.8443 (pptt) cc_final: 0.8228 (pttp) REVERT: D 82 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6625 (mp10) REVERT: E 24 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8011 (mtm110) REVERT: E 85 LEU cc_start: 0.8303 (tp) cc_final: 0.8098 (mm) REVERT: E 114 LEU cc_start: 0.2418 (OUTLIER) cc_final: 0.1633 (pp) REVERT: F 16 ARG cc_start: 0.8224 (mtt180) cc_final: 0.8020 (mtt90) REVERT: F 114 LEU cc_start: 0.2576 (OUTLIER) cc_final: 0.1877 (pp) REVERT: H 24 ARG cc_start: 0.8353 (mtp180) cc_final: 0.8031 (mtp-110) REVERT: H 39 GLU cc_start: 0.8383 (tt0) cc_final: 0.8048 (tt0) REVERT: H 45 LYS cc_start: 0.8419 (pptt) cc_final: 0.7725 (pptt) REVERT: H 85 LEU cc_start: 0.8322 (tp) cc_final: 0.7952 (mm) REVERT: H 114 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.1508 (pp) REVERT: I 14 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8869 (mm) REVERT: I 24 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8056 (mtm110) REVERT: I 114 LEU cc_start: 0.2764 (OUTLIER) cc_final: 0.2018 (pp) REVERT: J 85 LEU cc_start: 0.8552 (tp) cc_final: 0.8139 (mm) REVERT: K 39 GLU cc_start: 0.8361 (tt0) cc_final: 0.8043 (tt0) REVERT: K 45 LYS cc_start: 0.8421 (pptt) cc_final: 0.7752 (pptt) REVERT: K 82 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: K 114 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.1688 (pp) REVERT: L 24 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8102 (mtm110) REVERT: L 114 LEU cc_start: 0.3105 (OUTLIER) cc_final: 0.2340 (pp) REVERT: L 141 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8478 (ptt) REVERT: L 181 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8371 (tt0) outliers start: 35 outliers final: 15 residues processed: 357 average time/residue: 0.2185 time to fit residues: 112.4319 Evaluate side-chains 342 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 314 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 75 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 134 optimal weight: 0.0270 chunk 266 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114099 restraints weight = 34378.736| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3184 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26052 Z= 0.094 Angle : 0.469 6.477 35232 Z= 0.246 Chirality : 0.042 0.162 3684 Planarity : 0.003 0.028 4536 Dihedral : 3.948 19.138 3432 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.11 % Allowed : 13.19 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.15), residues: 3036 helix: 1.10 (0.15), residues: 1296 sheet: -2.55 (0.40), residues: 144 loop : -1.10 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 16 TYR 0.010 0.001 TYR G 72 PHE 0.009 0.001 PHE F 64 TRP 0.007 0.001 TRP E 22 HIS 0.001 0.000 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00215 (26052) covalent geometry : angle 0.46929 (35232) hydrogen bonds : bond 0.03375 ( 966) hydrogen bonds : angle 4.28271 ( 2826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 356 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8465 (pptt) cc_final: 0.7921 (pttp) REVERT: A 85 LEU cc_start: 0.8523 (tp) cc_final: 0.8038 (mm) REVERT: B 39 GLU cc_start: 0.8221 (tt0) cc_final: 0.7887 (tt0) REVERT: B 45 LYS cc_start: 0.8384 (pptt) cc_final: 0.7977 (pttp) REVERT: B 85 LEU cc_start: 0.8289 (tp) cc_final: 0.7989 (mm) REVERT: B 114 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.1971 (pp) REVERT: C 114 LEU cc_start: 0.2887 (OUTLIER) cc_final: 0.1982 (pp) REVERT: D 14 ILE cc_start: 0.8695 (mt) cc_final: 0.8397 (tt) REVERT: D 45 LYS cc_start: 0.8481 (pptt) cc_final: 0.8269 (pttp) REVERT: D 70 TYR cc_start: 0.7041 (m-80) cc_final: 0.6806 (m-80) REVERT: D 110 MET cc_start: 0.7644 (ptp) cc_final: 0.7389 (ptp) REVERT: E 24 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8247 (mtp-110) REVERT: E 45 LYS cc_start: 0.8297 (pptt) cc_final: 0.7728 (pptt) REVERT: E 85 LEU cc_start: 0.8323 (tp) cc_final: 0.8044 (mm) REVERT: E 114 LEU cc_start: 0.2492 (OUTLIER) cc_final: 0.1799 (pp) REVERT: F 45 LYS cc_start: 0.8469 (pptt) cc_final: 0.8056 (pptt) REVERT: F 114 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.2125 (pp) REVERT: H 24 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8203 (mtp-110) REVERT: H 39 GLU cc_start: 0.8162 (tt0) cc_final: 0.7830 (tt0) REVERT: H 85 LEU cc_start: 0.8274 (tp) cc_final: 0.7889 (mm) REVERT: H 114 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.1816 (pp) REVERT: I 14 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8916 (mm) REVERT: I 24 ARG cc_start: 0.8455 (mtp180) cc_final: 0.8174 (mtm110) REVERT: I 45 LYS cc_start: 0.8459 (pptt) cc_final: 0.8061 (pptt) REVERT: I 114 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2083 (pp) REVERT: I 145 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8466 (mt-10) REVERT: J 45 LYS cc_start: 0.8650 (pttp) cc_final: 0.8401 (pttp) REVERT: J 85 LEU cc_start: 0.8506 (tp) cc_final: 0.8091 (mm) REVERT: K 39 GLU cc_start: 0.8182 (tt0) cc_final: 0.7870 (tt0) REVERT: K 45 LYS cc_start: 0.8385 (pptt) cc_final: 0.7977 (pttp) REVERT: K 114 LEU cc_start: 0.2718 (OUTLIER) cc_final: 0.1875 (pp) REVERT: L 24 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8155 (mtm110) REVERT: L 114 LEU cc_start: 0.2970 (OUTLIER) cc_final: 0.2287 (pp) REVERT: L 181 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8260 (tt0) outliers start: 30 outliers final: 13 residues processed: 379 average time/residue: 0.2158 time to fit residues: 117.5696 Evaluate side-chains 360 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 337 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 227 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 285 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN I 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108593 restraints weight = 34346.000| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.28 r_work: 0.3120 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26052 Z= 0.168 Angle : 0.528 9.130 35232 Z= 0.278 Chirality : 0.044 0.158 3684 Planarity : 0.003 0.042 4536 Dihedral : 4.045 18.545 3432 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.19 % Allowed : 13.44 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.15), residues: 3036 helix: 1.03 (0.15), residues: 1308 sheet: -2.52 (0.40), residues: 144 loop : -1.06 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 16 TYR 0.011 0.001 TYR I 72 PHE 0.016 0.001 PHE F 64 TRP 0.009 0.001 TRP B 22 HIS 0.001 0.000 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00415 (26052) covalent geometry : angle 0.52844 (35232) hydrogen bonds : bond 0.04552 ( 966) hydrogen bonds : angle 4.48323 ( 2826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8387 (pptt) cc_final: 0.7892 (pttp) REVERT: A 85 LEU cc_start: 0.8539 (tp) cc_final: 0.8159 (mm) REVERT: B 39 GLU cc_start: 0.8381 (tt0) cc_final: 0.8045 (tt0) REVERT: B 45 LYS cc_start: 0.8372 (pptt) cc_final: 0.7738 (pptt) REVERT: B 85 LEU cc_start: 0.8358 (tp) cc_final: 0.8014 (mm) REVERT: B 114 LEU cc_start: 0.2624 (OUTLIER) cc_final: 0.1814 (pp) REVERT: C 82 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: C 114 LEU cc_start: 0.2621 (OUTLIER) cc_final: 0.1942 (pp) REVERT: C 145 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8640 (mt-10) REVERT: D 45 LYS cc_start: 0.8415 (pptt) cc_final: 0.8167 (pttp) REVERT: D 70 TYR cc_start: 0.7123 (m-80) cc_final: 0.6840 (m-80) REVERT: E 24 ARG cc_start: 0.8393 (mtp180) cc_final: 0.8071 (mtp-110) REVERT: E 45 LYS cc_start: 0.8305 (pptt) cc_final: 0.7731 (pptt) REVERT: E 114 LEU cc_start: 0.2423 (OUTLIER) cc_final: 0.1652 (pp) REVERT: F 45 LYS cc_start: 0.8503 (pptt) cc_final: 0.8129 (pptt) REVERT: F 114 LEU cc_start: 0.2702 (OUTLIER) cc_final: 0.2011 (pp) REVERT: H 24 ARG cc_start: 0.8289 (mtp180) cc_final: 0.7915 (mtm110) REVERT: H 45 LYS cc_start: 0.8392 (pptt) cc_final: 0.7739 (pptt) REVERT: H 85 LEU cc_start: 0.8288 (tp) cc_final: 0.7914 (mm) REVERT: H 114 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.1765 (pp) REVERT: I 14 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8877 (mm) REVERT: I 24 ARG cc_start: 0.8446 (mtp180) cc_final: 0.8087 (mtm110) REVERT: I 45 LYS cc_start: 0.8538 (pptt) cc_final: 0.8187 (pptt) REVERT: I 82 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: I 114 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2079 (pp) REVERT: J 14 ILE cc_start: 0.8708 (mt) cc_final: 0.8428 (tt) REVERT: J 45 LYS cc_start: 0.8664 (pttp) cc_final: 0.8416 (pttp) REVERT: J 85 LEU cc_start: 0.8520 (tp) cc_final: 0.8160 (mm) REVERT: K 39 GLU cc_start: 0.8369 (tt0) cc_final: 0.8038 (tt0) REVERT: K 45 LYS cc_start: 0.8379 (pptt) cc_final: 0.7748 (pptt) REVERT: K 114 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.1842 (pp) REVERT: L 24 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8082 (mtm110) REVERT: L 114 LEU cc_start: 0.3059 (OUTLIER) cc_final: 0.2307 (pp) REVERT: L 181 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8304 (tt0) outliers start: 32 outliers final: 15 residues processed: 348 average time/residue: 0.2193 time to fit residues: 108.7567 Evaluate side-chains 342 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 148 optimal weight: 0.0010 chunk 252 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN I 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111384 restraints weight = 34223.844| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.28 r_work: 0.3160 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26052 Z= 0.106 Angle : 0.483 9.581 35232 Z= 0.254 Chirality : 0.042 0.159 3684 Planarity : 0.003 0.033 4536 Dihedral : 3.943 19.776 3432 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.04 % Allowed : 13.70 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.15), residues: 3036 helix: 1.18 (0.15), residues: 1308 sheet: -2.51 (0.40), residues: 144 loop : -0.92 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 16 TYR 0.010 0.001 TYR E 72 PHE 0.010 0.001 PHE F 64 TRP 0.007 0.001 TRP B 22 HIS 0.001 0.000 HIS J 57 Details of bonding type rmsd covalent geometry : bond 0.00250 (26052) covalent geometry : angle 0.48284 (35232) hydrogen bonds : bond 0.03606 ( 966) hydrogen bonds : angle 4.28262 ( 2826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8429 (pptt) cc_final: 0.7895 (pttp) REVERT: A 85 LEU cc_start: 0.8535 (tp) cc_final: 0.8147 (mm) REVERT: B 39 GLU cc_start: 0.8302 (tt0) cc_final: 0.7945 (tt0) REVERT: B 45 LYS cc_start: 0.8373 (pptt) cc_final: 0.7989 (pttp) REVERT: B 85 LEU cc_start: 0.8320 (tp) cc_final: 0.7980 (mm) REVERT: B 114 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.1596 (pp) REVERT: C 45 LYS cc_start: 0.8446 (pptt) cc_final: 0.8088 (pptt) REVERT: C 82 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: C 114 LEU cc_start: 0.2666 (OUTLIER) cc_final: 0.2021 (pp) REVERT: D 45 LYS cc_start: 0.8459 (pptt) cc_final: 0.7958 (pttp) REVERT: D 70 TYR cc_start: 0.7120 (m-80) cc_final: 0.6861 (m-80) REVERT: D 85 LEU cc_start: 0.8523 (tp) cc_final: 0.8037 (mm) REVERT: D 110 MET cc_start: 0.7585 (ptp) cc_final: 0.7288 (ptp) REVERT: E 24 ARG cc_start: 0.8388 (mtp180) cc_final: 0.8096 (mtp-110) REVERT: E 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.7743 (pptt) REVERT: E 114 LEU cc_start: 0.2481 (OUTLIER) cc_final: 0.1771 (pp) REVERT: F 14 ILE cc_start: 0.9059 (mt) cc_final: 0.8811 (mm) REVERT: F 45 LYS cc_start: 0.8391 (pptt) cc_final: 0.8069 (pptt) REVERT: F 114 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.1931 (pp) REVERT: H 24 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8066 (mtp-110) REVERT: H 39 GLU cc_start: 0.8337 (tt0) cc_final: 0.7964 (tt0) REVERT: H 85 LEU cc_start: 0.8297 (tp) cc_final: 0.7881 (mm) REVERT: H 114 LEU cc_start: 0.2545 (OUTLIER) cc_final: 0.1837 (pp) REVERT: I 14 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8874 (mm) REVERT: I 24 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8071 (mtm110) REVERT: I 45 LYS cc_start: 0.8446 (pptt) cc_final: 0.8226 (pttp) REVERT: I 82 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: I 114 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2136 (pp) REVERT: J 45 LYS cc_start: 0.8635 (pttp) cc_final: 0.8374 (pttp) REVERT: J 85 LEU cc_start: 0.8509 (tp) cc_final: 0.8148 (mm) REVERT: K 45 LYS cc_start: 0.8376 (pptt) cc_final: 0.7764 (pptt) REVERT: K 114 LEU cc_start: 0.2677 (OUTLIER) cc_final: 0.1836 (pp) REVERT: L 24 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8085 (mtm110) REVERT: L 45 LYS cc_start: 0.8392 (pptt) cc_final: 0.7976 (pptt) REVERT: L 114 LEU cc_start: 0.2925 (OUTLIER) cc_final: 0.2235 (pp) REVERT: L 181 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8277 (tt0) outliers start: 28 outliers final: 13 residues processed: 354 average time/residue: 0.2139 time to fit residues: 108.3770 Evaluate side-chains 348 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 259 optimal weight: 0.0000 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 266 optimal weight: 0.0370 chunk 161 optimal weight: 3.9990 overall best weight: 2.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN G 82 GLN J 82 GLN L 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108142 restraints weight = 34268.806| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.25 r_work: 0.3113 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26052 Z= 0.180 Angle : 0.532 8.810 35232 Z= 0.281 Chirality : 0.045 0.151 3684 Planarity : 0.003 0.042 4536 Dihedral : 4.067 18.284 3432 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.30 % Allowed : 13.59 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.15), residues: 3036 helix: 1.14 (0.15), residues: 1296 sheet: -2.52 (0.40), residues: 144 loop : -0.95 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 16 TYR 0.012 0.001 TYR I 72 PHE 0.017 0.001 PHE F 64 TRP 0.009 0.002 TRP B 22 HIS 0.001 0.000 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00444 (26052) covalent geometry : angle 0.53199 (35232) hydrogen bonds : bond 0.04702 ( 966) hydrogen bonds : angle 4.50482 ( 2826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6260.76 seconds wall clock time: 107 minutes 30.76 seconds (6450.76 seconds total)