Starting phenix.real_space_refine on Mon Aug 25 20:02:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.map" model { file = "/net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cku_45654/08_2025/9cku_45654.cif" } resolution = 2.04 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= 0.003 sd= 1.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 9534 2.51 5 N 2721 2.21 5 O 2992 1.98 5 H 15361 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30660 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4070 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 261, 3972 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 250} Conformer: "A" Number of residues, atoms: 252, 3858 Classifications: {'peptide': 252} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 bond proxies already assigned to first conformer: 3791 Chain: "B" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 3972 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 4070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 3972 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 250} Conformer: "B" Number of residues, atoms: 253, 3877 Classifications: {'peptide': 253} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 bond proxies already assigned to first conformer: 3810 Chain: "D" Number of atoms: 4089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 3972 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 250} Conformer: "B" Number of residues, atoms: 253, 3877 Classifications: {'peptide': 253} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 bond proxies already assigned to first conformer: 3791 Chain: "E" Number of atoms: 4070 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 261, 3972 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 250} Conformer: "A" Number of residues, atoms: 252, 3858 Classifications: {'peptide': 252} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 bond proxies already assigned to first conformer: 3791 Chain: "F" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 3878 Classifications: {'peptide': 254} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 1 Chain: "G" Number of atoms: 5928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 5928 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 1 Chain: "H" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 453 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Residues with excluded nonbonded symmetry interactions: 55 residue: pdb=" N BALA A 162 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 162 " occ=0.50 residue: pdb=" N BALA A 163 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 163 " occ=0.50 residue: pdb=" N BALA A 164 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 164 " occ=0.50 residue: pdb=" N BALA A 165 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 165 " occ=0.50 residue: pdb=" N BARG A 166 " occ=0.50 ... (22 atoms not shown) pdb="HH22BARG A 166 " occ=0.50 residue: pdb=" N BSER A 167 " occ=0.50 ... (9 atoms not shown) pdb=" HG BSER A 167 " occ=0.50 residue: pdb=" N BALA A 168 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 168 " occ=0.50 residue: pdb=" N BALA A 169 " occ=0.50 ... (8 atoms not shown) pdb=" HB3BALA A 169 " occ=0.50 residue: pdb=" N BLEU A 170 " occ=0.50 ... (17 atoms not shown) pdb="HD23BLEU A 170 " occ=0.50 residue: pdb=" N AARG A 171 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 171 " occ=0.50 residue: pdb=" N AARG A 172 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 172 " occ=0.50 residue: pdb=" N AVAL A 173 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A 173 " occ=0.50 ... (remaining 43 not shown) Time building chain proxies: 7.96, per 1000 atoms: 0.26 Number of scatterers: 30660 At special positions: 0 Unit cell: (99.825, 111.375, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 2992 8.00 N 2721 7.00 C 9534 6.00 H 15361 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 17 sheets defined 48.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.658A pdb=" N GLU A 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 124 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.185A pdb=" N BSER A 167 " --> pdb=" O BALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.664A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.509A pdb=" N GLU B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 159 through 167 removed outlier: 4.119A pdb=" N SER B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.643A pdb=" N LEU B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.517A pdb=" N GLU C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 58 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.081A pdb=" N ASER C 167 " --> pdb=" O AALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 213 Processing helix chain 'C' and resid 230 through 235 removed outlier: 3.600A pdb=" N LEU C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 39 through 52 Processing helix chain 'D' and resid 53 through 58 removed outlier: 3.571A pdb=" N GLU D 56 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 58 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 159 through 167 removed outlier: 3.996A pdb=" N ASER D 167 " --> pdb=" O AALA D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 Processing helix chain 'D' and resid 230 through 235 removed outlier: 3.711A pdb=" N LEU D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.621A pdb=" N LEU E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 109 through 124 Processing helix chain 'E' and resid 159 through 167 removed outlier: 4.176A pdb=" N BSER E 167 " --> pdb=" O BALA E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 213 Processing helix chain 'E' and resid 230 through 235 removed outlier: 3.598A pdb=" N LEU E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 39 through 52 Processing helix chain 'F' and resid 53 through 58 removed outlier: 3.671A pdb=" N GLU F 56 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 109 through 124 Processing helix chain 'F' and resid 185 through 213 Processing helix chain 'F' and resid 230 through 235 Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'G' and resid 22 through 39 Processing helix chain 'G' and resid 108 through 132 Processing helix chain 'G' and resid 166 through 181 Proline residue: G 176 - end of helix Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.163A pdb=" N ASP G 208 " --> pdb=" O GLN G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 251 through 271 removed outlier: 3.649A pdb=" N THR G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 282 through 292 removed outlier: 3.600A pdb=" N HIS G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 327 Processing helix chain 'G' and resid 331 through 351 Processing helix chain 'G' and resid 352 through 356 Processing helix chain 'G' and resid 359 through 376 Processing helix chain 'G' and resid 381 through 392 removed outlier: 4.436A pdb=" N SER G 392 " --> pdb=" O ASP G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 407 Processing helix chain 'G' and resid 415 through 423 Processing helix chain 'H' and resid 36 through 47 removed outlier: 3.768A pdb=" N VAL H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33 removed outlier: 5.434A pdb=" N VAL A 26 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 18 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 61 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE A 90 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 63 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154 removed outlier: 6.602A pdb=" N VAL A 140 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 150 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 138 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 152 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 136 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33 removed outlier: 5.613A pdb=" N VAL B 26 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 18 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 61 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE B 90 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 63 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154 removed outlier: 3.926A pdb=" N GLY B 149 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33 removed outlier: 5.556A pdb=" N VAL C 26 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER C 18 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154 removed outlier: 3.941A pdb=" N GLY C 149 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33 removed outlier: 5.592A pdb=" N VAL D 26 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER D 18 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR D 61 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154 removed outlier: 3.936A pdb=" N GLY D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 33 removed outlier: 5.555A pdb=" N VAL E 26 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER E 18 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 154 removed outlier: 6.316A pdb=" N VAL E 140 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL E 138 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE E 152 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE E 136 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 25 through 33 removed outlier: 5.514A pdb=" N VAL F 26 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER F 18 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR F 61 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 154 removed outlier: 4.055A pdb=" N GLY F 149 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AB5, first strand: chain 'G' and resid 12 through 14 Processing sheet with id=AB6, first strand: chain 'G' and resid 189 through 192 removed outlier: 6.025A pdb=" N GLY G 200 " --> pdb=" O GLY G 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 210 through 215 removed outlier: 7.256A pdb=" N ILE G 224 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU G 213 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN G 226 " --> pdb=" O GLU G 213 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 299 through 301 860 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15341 1.03 - 1.23: 314 1.23 - 1.43: 5920 1.43 - 1.62: 9117 1.62 - 1.82: 84 Bond restraints: 30776 Sorted by residual: bond pdb=" N GLY F 193 " pdb=" CA GLY F 193 " ideal model delta sigma weight residual 1.454 1.436 0.017 1.29e-02 6.01e+03 1.83e+00 bond pdb=" CB VAL B 173 " pdb=" CG2 VAL B 173 " ideal model delta sigma weight residual 1.521 1.557 -0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" C GLY F 193 " pdb=" O GLY F 193 " ideal model delta sigma weight residual 1.234 1.221 0.013 1.20e-02 6.94e+03 1.10e+00 bond pdb=" CB VAL F 85 " pdb=" CG1 VAL F 85 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" N GLY E 150 " pdb=" CA GLY E 150 " ideal model delta sigma weight residual 1.455 1.444 0.011 1.05e-02 9.07e+03 1.08e+00 ... (remaining 30771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 55753 5.38 - 10.76: 19 10.76 - 16.13: 2 16.13 - 21.51: 0 21.51 - 26.89: 9 Bond angle restraints: 55783 Sorted by residual: angle pdb=" CG1AVAL C 173 " pdb=" CB AVAL C 173 " pdb=" HB AVAL C 173 " ideal model delta sigma weight residual 108.00 81.11 26.89 3.00e+00 1.11e-01 8.03e+01 angle pdb=" CG1 VAL B 173 " pdb=" CB VAL B 173 " pdb=" HB VAL B 173 " ideal model delta sigma weight residual 108.00 81.12 26.88 3.00e+00 1.11e-01 8.03e+01 angle pdb=" CG2AVAL C 173 " pdb=" CB AVAL C 173 " pdb=" HB AVAL C 173 " ideal model delta sigma weight residual 108.00 81.15 26.85 3.00e+00 1.11e-01 8.01e+01 angle pdb=" CG2 VAL B 173 " pdb=" CB VAL B 173 " pdb=" HB VAL B 173 " ideal model delta sigma weight residual 108.00 81.17 26.83 3.00e+00 1.11e-01 8.00e+01 angle pdb=" CG2AVAL D 173 " pdb=" CB AVAL D 173 " pdb=" HB AVAL D 173 " ideal model delta sigma weight residual 108.00 81.28 26.72 3.00e+00 1.11e-01 7.93e+01 ... (remaining 55778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13332 17.71 - 35.42: 606 35.42 - 53.13: 261 53.13 - 70.84: 83 70.84 - 88.56: 10 Dihedral angle restraints: 14292 sinusoidal: 7954 harmonic: 6338 Sorted by residual: dihedral pdb=" CA ASN G 88 " pdb=" C ASN G 88 " pdb=" N GLY G 89 " pdb=" CA GLY G 89 " ideal model delta harmonic sigma weight residual 180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR G 153 " pdb=" C TYR G 153 " pdb=" N GLY G 154 " pdb=" CA GLY G 154 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP G 247 " pdb=" C ASP G 247 " pdb=" N ALA G 248 " pdb=" CA ALA G 248 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 14289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 2510 0.273 - 0.547: 0 0.547 - 0.820: 0 0.820 - 1.094: 0 1.094 - 1.367: 3 Chirality restraints: 2513 Sorted by residual: chirality pdb=" CB AVAL D 173 " pdb=" CA AVAL D 173 " pdb=" CG1AVAL D 173 " pdb=" CG2AVAL D 173 " both_signs ideal model delta sigma weight residual False -2.63 -1.26 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CB AVAL C 173 " pdb=" CA AVAL C 173 " pdb=" CG1AVAL C 173 " pdb=" CG2AVAL C 173 " both_signs ideal model delta sigma weight residual False -2.63 -1.28 -1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -1.31 -1.32 2.00e-01 2.50e+01 4.38e+01 ... (remaining 2510 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 210 " -0.076 9.50e-02 1.11e+02 3.59e-02 1.51e+01 pdb=" NE ARG F 210 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG F 210 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG F 210 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 210 " -0.050 2.00e-02 2.50e+03 pdb="HH11 ARG F 210 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 210 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG F 210 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 210 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 210 " -0.132 9.50e-02 1.11e+02 5.00e-02 1.48e+01 pdb=" NE ARG D 210 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG D 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 210 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 210 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG D 210 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG D 210 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG D 210 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG D 210 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 210 " -0.140 9.50e-02 1.11e+02 5.13e-02 1.26e+01 pdb=" NE ARG E 210 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG E 210 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 210 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 210 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG E 210 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 210 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG E 210 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG E 210 " 0.038 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1273 2.19 - 2.79: 62675 2.79 - 3.39: 88340 3.39 - 4.00: 119961 4.00 - 4.60: 180923 Nonbonded interactions: 453172 Sorted by model distance: nonbonded pdb=" OE1AGLU C 174 " pdb=" H AGLU C 174 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU B 174 " pdb=" H GLU B 174 " model vdw 1.607 2.450 nonbonded pdb=" O AARG C 166 " pdb=" HG ASER C 167 " model vdw 1.631 2.450 nonbonded pdb=" OD2 ASP G 116 " pdb=" HZ3 LYS G 143 " model vdw 1.643 2.450 nonbonded pdb=" O ARG B 166 " pdb=" HG SER B 167 " model vdw 1.669 2.450 ... (remaining 453167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ h 261)) selection = (chain 'B' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ h 261)) selection = (chain 'C' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ h 261)) selection = (chain 'D' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ h 261)) selection = (chain 'E' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ h 261)) selection = (chain 'F' and (resid 1 through 161 or resid 176 through 261)) } 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=0.50 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: 3.160 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: 0.230 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15415 Z= 0.211 Angle : 0.674 10.989 20966 Z= 0.374 Chirality : 0.068 1.367 2513 Planarity : 0.006 0.083 2728 Dihedral : 11.841 88.556 5621 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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 aren not related in a simple way. whole: 1.44 (0.18), residues: 1974 helix: 2.06 (0.18), residues: 735 sheet: 1.16 (0.24), residues: 393 loop : -0.09 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 210 TYR 0.014 0.002 TYR G 34 PHE 0.016 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00445 (15415) covalent geometry : angle 0.67354 (20966) hydrogen bonds : bond 0.10345 ( 860) hydrogen bonds : angle 5.81079 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8182 (mtp) cc_final: 0.7818 (mtm) REVERT: A 21 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7882 (mmmm) REVERT: A 91 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7627 (tp30) REVERT: B 1 MET cc_start: 0.8475 (mtp) cc_final: 0.8270 (mtp) REVERT: B 23 HIS cc_start: 0.7773 (m-70) cc_final: 0.7472 (m90) REVERT: B 87 HIS cc_start: 0.8449 (p90) cc_final: 0.7799 (m90) REVERT: C 20 MET cc_start: 0.7855 (mtp) cc_final: 0.7410 (mmt) REVERT: C 87 HIS cc_start: 0.8240 (p90) cc_final: 0.7793 (m-70) REVERT: D 20 MET cc_start: 0.7685 (mtp) cc_final: 0.7041 (mpt) REVERT: D 87 HIS cc_start: 0.8350 (p90) cc_final: 0.7948 (m-70) REVERT: D 259 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7161 (mtt-85) REVERT: E 53 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7607 (mp0) REVERT: E 87 HIS cc_start: 0.8533 (p90) cc_final: 0.7900 (m90) REVERT: F 23 HIS cc_start: 0.7902 (m-70) cc_final: 0.7623 (m90) REVERT: F 53 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7727 (mp0) REVERT: F 144 LYS cc_start: 0.8326 (mttt) cc_final: 0.7950 (mtmt) REVERT: F 230 THR cc_start: 0.8818 (p) cc_final: 0.8559 (t) outliers start: 0 outliers final: 1 residues processed: 239 average time/residue: 1.7374 time to fit residues: 450.2959 Evaluate side-chains 208 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 72 HIS E 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112866 restraints weight = 54115.084| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.36 r_work: 0.3052 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15415 Z= 0.174 Angle : 0.580 11.310 20966 Z= 0.319 Chirality : 0.066 1.395 2513 Planarity : 0.006 0.049 2728 Dihedral : 4.773 27.358 2163 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.61 % Allowed : 7.22 % Favored : 92.17 % 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 aren not related in a simple way. whole: 1.28 (0.17), residues: 1974 helix: 1.92 (0.18), residues: 746 sheet: 1.16 (0.25), residues: 372 loop : -0.23 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 179 TYR 0.016 0.002 TYR G 34 PHE 0.017 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.012 0.001 HIS G 129 Details of bonding type rmsd covalent geometry : bond 0.00360 (15415) covalent geometry : angle 0.57971 (20966) hydrogen bonds : bond 0.05508 ( 860) hydrogen bonds : angle 5.47640 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8205 (mtp) cc_final: 0.7842 (mtm) REVERT: A 21 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7785 (mmmm) REVERT: A 91 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7617 (tp30) REVERT: B 23 HIS cc_start: 0.7782 (m-70) cc_final: 0.7455 (m90) REVERT: B 87 HIS cc_start: 0.8513 (p90) cc_final: 0.7711 (m90) REVERT: B 260 ASN cc_start: 0.8402 (m-40) cc_final: 0.8158 (m110) REVERT: C 20 MET cc_start: 0.7924 (mtp) cc_final: 0.7481 (mmt) REVERT: C 29 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: C 87 HIS cc_start: 0.8378 (p90) cc_final: 0.7860 (m-70) REVERT: D 20 MET cc_start: 0.7705 (mtp) cc_final: 0.7096 (mpt) REVERT: D 87 HIS cc_start: 0.8417 (p90) cc_final: 0.7913 (m-70) REVERT: D 259 ARG cc_start: 0.7598 (ttt90) cc_final: 0.7109 (mtt-85) REVERT: F 23 HIS cc_start: 0.7894 (m-70) cc_final: 0.7613 (m90) REVERT: F 53 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7737 (mp0) REVERT: F 144 LYS cc_start: 0.8393 (mttt) cc_final: 0.7963 (mtmt) REVERT: G 239 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7895 (tmt90) outliers start: 9 outliers final: 5 residues processed: 213 average time/residue: 1.8516 time to fit residues: 426.3916 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113126 restraints weight = 61546.929| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.46 r_work: 0.3045 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15415 Z= 0.150 Angle : 0.544 11.199 20966 Z= 0.298 Chirality : 0.066 1.415 2513 Planarity : 0.005 0.044 2728 Dihedral : 4.641 26.548 2163 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.80 % Allowed : 7.47 % Favored : 91.74 % 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 aren not related in a simple way. whole: 1.37 (0.18), residues: 1974 helix: 2.05 (0.18), residues: 746 sheet: 1.19 (0.25), residues: 372 loop : -0.21 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 179 TYR 0.013 0.002 TYR G 34 PHE 0.015 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.008 0.001 HIS G 129 Details of bonding type rmsd covalent geometry : bond 0.00307 (15415) covalent geometry : angle 0.54407 (20966) hydrogen bonds : bond 0.05185 ( 860) hydrogen bonds : angle 5.33374 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8190 (mtp) cc_final: 0.7822 (mtm) REVERT: A 21 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7780 (mmmm) REVERT: A 91 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7611 (tp30) REVERT: B 23 HIS cc_start: 0.7753 (m-70) cc_final: 0.7413 (m90) REVERT: B 260 ASN cc_start: 0.8378 (m-40) cc_final: 0.8122 (m110) REVERT: C 20 MET cc_start: 0.7924 (mtp) cc_final: 0.7467 (mmt) REVERT: C 29 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: C 87 HIS cc_start: 0.8383 (p90) cc_final: 0.7858 (m-70) REVERT: D 20 MET cc_start: 0.7709 (mtp) cc_final: 0.7078 (mpt) REVERT: D 87 HIS cc_start: 0.8418 (p90) cc_final: 0.7871 (m-70) REVERT: D 259 ARG cc_start: 0.7601 (ttt90) cc_final: 0.7099 (mtt-85) REVERT: E 20 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7862 (mpt) REVERT: F 23 HIS cc_start: 0.7873 (m-70) cc_final: 0.7584 (m90) REVERT: F 53 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7730 (mp0) REVERT: F 144 LYS cc_start: 0.8410 (mttt) cc_final: 0.7967 (mtmt) outliers start: 12 outliers final: 6 residues processed: 212 average time/residue: 1.5845 time to fit residues: 364.1439 Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 95 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 GLN D 72 HIS D 104 ASN H 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111622 restraints weight = 56973.542| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.41 r_work: 0.3076 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15415 Z= 0.193 Angle : 0.595 11.142 20966 Z= 0.329 Chirality : 0.066 1.407 2513 Planarity : 0.006 0.058 2728 Dihedral : 4.870 28.643 2163 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.80 % Allowed : 7.77 % Favored : 91.43 % 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 aren not related in a simple way. whole: 1.14 (0.17), residues: 1974 helix: 1.81 (0.18), residues: 746 sheet: 1.15 (0.25), residues: 381 loop : -0.35 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 179 TYR 0.016 0.002 TYR G 34 PHE 0.019 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00402 (15415) covalent geometry : angle 0.59460 (20966) hydrogen bonds : bond 0.05849 ( 860) hydrogen bonds : angle 5.53831 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8203 (mtp) cc_final: 0.7814 (mtm) REVERT: A 21 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7793 (mmmm) REVERT: A 91 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7618 (tp30) REVERT: B 23 HIS cc_start: 0.7772 (m-70) cc_final: 0.7440 (m90) REVERT: B 106 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7495 (mptt) REVERT: B 260 ASN cc_start: 0.8378 (m-40) cc_final: 0.8136 (m110) REVERT: C 20 MET cc_start: 0.7926 (mtp) cc_final: 0.7480 (mmt) REVERT: C 29 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: C 87 HIS cc_start: 0.8403 (p90) cc_final: 0.7887 (m90) REVERT: D 20 MET cc_start: 0.7746 (mtp) cc_final: 0.7108 (mpt) REVERT: D 87 HIS cc_start: 0.8426 (p90) cc_final: 0.7885 (m-70) REVERT: D 259 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7132 (mtt-85) REVERT: F 23 HIS cc_start: 0.7892 (m-70) cc_final: 0.7614 (m90) REVERT: F 53 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7778 (mp0) REVERT: F 144 LYS cc_start: 0.8408 (mttt) cc_final: 0.7982 (mtmt) outliers start: 11 outliers final: 7 residues processed: 214 average time/residue: 1.7586 time to fit residues: 406.7631 Evaluate side-chains 211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 344 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 191 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 overall best weight: 1.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS H 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112596 restraints weight = 61196.755| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.46 r_work: 0.3075 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15415 Z= 0.145 Angle : 0.537 11.135 20966 Z= 0.294 Chirality : 0.066 1.416 2513 Planarity : 0.005 0.046 2728 Dihedral : 4.651 27.674 2163 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.73 % Allowed : 7.89 % Favored : 91.37 % 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 aren not related in a simple way. whole: 1.34 (0.18), residues: 1974 helix: 2.03 (0.18), residues: 746 sheet: 1.19 (0.25), residues: 372 loop : -0.26 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 179 TYR 0.013 0.002 TYR G 34 PHE 0.015 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00297 (15415) covalent geometry : angle 0.53698 (20966) hydrogen bonds : bond 0.05031 ( 860) hydrogen bonds : angle 5.29231 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8154 (mtp) cc_final: 0.7774 (mtm) REVERT: A 21 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7778 (mmtm) REVERT: A 91 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7589 (tp30) REVERT: B 23 HIS cc_start: 0.7724 (m-70) cc_final: 0.7383 (m90) REVERT: B 260 ASN cc_start: 0.8380 (m-40) cc_final: 0.8123 (m110) REVERT: C 20 MET cc_start: 0.7926 (mtp) cc_final: 0.7471 (mmt) REVERT: C 29 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 87 HIS cc_start: 0.8376 (p90) cc_final: 0.7892 (m90) REVERT: C 179 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7756 (ptp-170) REVERT: D 20 MET cc_start: 0.7755 (mtp) cc_final: 0.7114 (mpt) REVERT: D 87 HIS cc_start: 0.8410 (p90) cc_final: 0.7864 (m-70) REVERT: D 259 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7116 (mtt-85) REVERT: F 23 HIS cc_start: 0.7834 (m-70) cc_final: 0.7530 (m90) REVERT: F 144 LYS cc_start: 0.8398 (mttt) cc_final: 0.7964 (mtmt) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 1.5948 time to fit residues: 362.6382 Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS D 104 ASN G 373 GLN H 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111503 restraints weight = 59435.655| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.44 r_work: 0.3070 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15415 Z= 0.189 Angle : 0.589 11.251 20966 Z= 0.325 Chirality : 0.066 1.409 2513 Planarity : 0.005 0.053 2728 Dihedral : 4.832 29.118 2163 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.22 % Allowed : 7.83 % Favored : 90.94 % 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 aren not related in a simple way. whole: 1.16 (0.17), residues: 1974 helix: 1.85 (0.18), residues: 746 sheet: 1.15 (0.25), residues: 381 loop : -0.36 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 179 TYR 0.016 0.002 TYR G 34 PHE 0.019 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00393 (15415) covalent geometry : angle 0.58898 (20966) hydrogen bonds : bond 0.05748 ( 860) hydrogen bonds : angle 5.49868 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8172 (mtp) cc_final: 0.7787 (mtm) REVERT: A 21 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7780 (mmtm) REVERT: A 91 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7627 (tp30) REVERT: B 23 HIS cc_start: 0.7746 (m-70) cc_final: 0.7419 (m90) REVERT: B 106 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7487 (mptt) REVERT: B 260 ASN cc_start: 0.8389 (m-40) cc_final: 0.8133 (m110) REVERT: C 20 MET cc_start: 0.7917 (mtp) cc_final: 0.7466 (mmt) REVERT: C 29 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: C 87 HIS cc_start: 0.8409 (p90) cc_final: 0.7891 (m90) REVERT: C 179 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7752 (ptp-170) REVERT: D 20 MET cc_start: 0.7733 (mtp) cc_final: 0.7066 (mpt) REVERT: D 87 HIS cc_start: 0.8423 (p90) cc_final: 0.7870 (m-70) REVERT: D 259 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7129 (mtt-85) REVERT: F 23 HIS cc_start: 0.7829 (m-70) cc_final: 0.7536 (m90) REVERT: F 144 LYS cc_start: 0.8415 (mttt) cc_final: 0.7964 (mtmt) REVERT: G 239 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7855 (ttt90) outliers start: 18 outliers final: 7 residues processed: 213 average time/residue: 1.5587 time to fit residues: 359.4508 Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 239 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS G 373 GLN H 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112506 restraints weight = 60585.472| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.45 r_work: 0.3055 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15415 Z= 0.148 Angle : 0.542 11.129 20966 Z= 0.297 Chirality : 0.065 1.410 2513 Planarity : 0.005 0.057 2728 Dihedral : 4.671 28.284 2163 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.80 % Allowed : 8.38 % Favored : 90.82 % 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 aren not related in a simple way. whole: 1.31 (0.18), residues: 1974 helix: 2.02 (0.18), residues: 746 sheet: 1.19 (0.25), residues: 372 loop : -0.28 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.013 0.002 TYR G 34 PHE 0.015 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00306 (15415) covalent geometry : angle 0.54207 (20966) hydrogen bonds : bond 0.05065 ( 860) hydrogen bonds : angle 5.30260 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8147 (mtp) cc_final: 0.7767 (mtm) REVERT: A 21 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7784 (mmtm) REVERT: A 91 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7608 (tp30) REVERT: B 23 HIS cc_start: 0.7717 (m-70) cc_final: 0.7374 (m90) REVERT: B 260 ASN cc_start: 0.8389 (m-40) cc_final: 0.8124 (m110) REVERT: C 20 MET cc_start: 0.7914 (mtp) cc_final: 0.7467 (mmt) REVERT: C 29 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: C 87 HIS cc_start: 0.8375 (p90) cc_final: 0.7889 (m90) REVERT: C 179 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7751 (ptp-170) REVERT: D 20 MET cc_start: 0.7720 (mtp) cc_final: 0.7066 (mpt) REVERT: D 87 HIS cc_start: 0.8403 (p90) cc_final: 0.7813 (m-70) REVERT: D 259 ARG cc_start: 0.7613 (ttt90) cc_final: 0.7117 (mtt-85) REVERT: F 23 HIS cc_start: 0.7853 (m-70) cc_final: 0.7564 (m90) REVERT: F 53 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: F 144 LYS cc_start: 0.8400 (mttt) cc_final: 0.7956 (mtmt) outliers start: 11 outliers final: 6 residues processed: 211 average time/residue: 1.8674 time to fit residues: 425.9580 Evaluate side-chains 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS D 104 ASN G 373 GLN H 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111840 restraints weight = 65262.744| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.67 r_work: 0.3035 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15415 Z= 0.167 Angle : 0.566 11.193 20966 Z= 0.311 Chirality : 0.065 1.401 2513 Planarity : 0.005 0.077 2728 Dihedral : 4.751 29.231 2163 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.92 % Allowed : 8.51 % Favored : 90.58 % 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 aren not related in a simple way. whole: 1.22 (0.17), residues: 1974 helix: 1.93 (0.18), residues: 746 sheet: 1.15 (0.25), residues: 381 loop : -0.34 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 179 TYR 0.014 0.002 TYR G 34 PHE 0.018 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00346 (15415) covalent geometry : angle 0.56601 (20966) hydrogen bonds : bond 0.05421 ( 860) hydrogen bonds : angle 5.40506 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8142 (mtp) cc_final: 0.7765 (mtm) REVERT: A 21 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7779 (mmtm) REVERT: A 91 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7644 (tp30) REVERT: B 23 HIS cc_start: 0.7778 (m-70) cc_final: 0.7444 (m90) REVERT: B 260 ASN cc_start: 0.8399 (m-40) cc_final: 0.8129 (m110) REVERT: C 20 MET cc_start: 0.7919 (mtp) cc_final: 0.7459 (mmt) REVERT: C 29 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: C 87 HIS cc_start: 0.8407 (p90) cc_final: 0.7880 (m90) REVERT: C 179 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7763 (ptp-170) REVERT: D 20 MET cc_start: 0.7720 (mtp) cc_final: 0.7060 (mpt) REVERT: D 87 HIS cc_start: 0.8430 (p90) cc_final: 0.7834 (m-70) REVERT: D 259 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7117 (mtt-85) REVERT: F 23 HIS cc_start: 0.7837 (m-70) cc_final: 0.7553 (m90) REVERT: F 144 LYS cc_start: 0.8415 (mttt) cc_final: 0.7954 (mtmt) REVERT: H 46 VAL cc_start: 0.7478 (t) cc_final: 0.7203 (p) outliers start: 13 outliers final: 8 residues processed: 212 average time/residue: 1.7553 time to fit residues: 403.6115 Evaluate side-chains 211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 28 GLN D 72 HIS G 373 GLN H 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117584 restraints weight = 59782.036| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.40 r_work: 0.3086 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15415 Z= 0.120 Angle : 0.513 11.257 20966 Z= 0.278 Chirality : 0.065 1.422 2513 Planarity : 0.004 0.061 2728 Dihedral : 4.469 26.058 2163 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.73 % Allowed : 8.75 % Favored : 90.51 % 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 aren not related in a simple way. whole: 1.48 (0.18), residues: 1974 helix: 2.22 (0.18), residues: 746 sheet: 1.20 (0.25), residues: 372 loop : -0.20 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 179 TYR 0.009 0.002 TYR G 34 PHE 0.012 0.001 PHE E 198 TRP 0.011 0.001 TRP A 30 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00247 (15415) covalent geometry : angle 0.51266 (20966) hydrogen bonds : bond 0.04510 ( 860) hydrogen bonds : angle 5.13361 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8118 (mtp) cc_final: 0.7761 (mtm) REVERT: A 21 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7825 (mmtm) REVERT: A 91 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7621 (tp30) REVERT: A 144 LYS cc_start: 0.8773 (mttt) cc_final: 0.8385 (mtmm) REVERT: B 23 HIS cc_start: 0.7746 (m-70) cc_final: 0.7418 (m90) REVERT: B 260 ASN cc_start: 0.8375 (m-40) cc_final: 0.8114 (m110) REVERT: C 20 MET cc_start: 0.7923 (mtp) cc_final: 0.7489 (mmt) REVERT: C 29 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 87 HIS cc_start: 0.8345 (p90) cc_final: 0.7887 (m90) REVERT: D 20 MET cc_start: 0.7705 (mtp) cc_final: 0.7081 (mpt) REVERT: D 87 HIS cc_start: 0.8412 (p90) cc_final: 0.7853 (m90) REVERT: D 259 ARG cc_start: 0.7616 (ttt90) cc_final: 0.7140 (mtt-85) REVERT: E 91 GLU cc_start: 0.7043 (mp0) cc_final: 0.6572 (pm20) REVERT: F 23 HIS cc_start: 0.7859 (m-70) cc_final: 0.7582 (m90) REVERT: F 144 LYS cc_start: 0.8375 (mttt) cc_final: 0.7951 (mtmt) REVERT: H 46 VAL cc_start: 0.7503 (t) cc_final: 0.7238 (p) outliers start: 9 outliers final: 6 residues processed: 215 average time/residue: 1.8602 time to fit residues: 432.5044 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 72 HIS D 104 ASN G 373 GLN H 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114514 restraints weight = 62904.567| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.60 r_work: 0.3080 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15415 Z= 0.119 Angle : 0.509 11.088 20966 Z= 0.276 Chirality : 0.065 1.422 2513 Planarity : 0.004 0.068 2728 Dihedral : 4.415 26.449 2163 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.80 % Allowed : 8.87 % Favored : 90.33 % 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 aren not related in a simple way. whole: 1.53 (0.18), residues: 1974 helix: 2.28 (0.18), residues: 746 sheet: 1.18 (0.25), residues: 372 loop : -0.16 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 179 TYR 0.010 0.002 TYR G 256 PHE 0.012 0.001 PHE E 198 TRP 0.010 0.001 TRP A 30 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00243 (15415) covalent geometry : angle 0.50923 (20966) hydrogen bonds : bond 0.04505 ( 860) hydrogen bonds : angle 5.09868 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8157 (mtp) cc_final: 0.7761 (mtm) REVERT: A 21 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7765 (mmmm) REVERT: A 91 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7601 (tp30) REVERT: A 144 LYS cc_start: 0.8767 (mttt) cc_final: 0.8354 (mtmm) REVERT: B 23 HIS cc_start: 0.7704 (m-70) cc_final: 0.7377 (m90) REVERT: B 260 ASN cc_start: 0.8381 (m-40) cc_final: 0.8118 (m110) REVERT: C 20 MET cc_start: 0.7913 (mtp) cc_final: 0.7451 (mmt) REVERT: C 29 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: C 87 HIS cc_start: 0.8355 (p90) cc_final: 0.7871 (m90) REVERT: C 179 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7772 (ptp-170) REVERT: D 20 MET cc_start: 0.7690 (mtp) cc_final: 0.7040 (mpt) REVERT: D 87 HIS cc_start: 0.8418 (p90) cc_final: 0.7849 (m90) REVERT: D 259 ARG cc_start: 0.7592 (ttt90) cc_final: 0.7078 (mtt-85) REVERT: E 87 HIS cc_start: 0.8644 (p90) cc_final: 0.7987 (m90) REVERT: F 23 HIS cc_start: 0.7836 (m-70) cc_final: 0.7560 (m90) REVERT: F 144 LYS cc_start: 0.8359 (mttt) cc_final: 0.7918 (mtmt) REVERT: G 8 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7090 (mt-10) REVERT: H 46 VAL cc_start: 0.7431 (t) cc_final: 0.7140 (p) outliers start: 10 outliers final: 6 residues processed: 209 average time/residue: 1.7716 time to fit residues: 400.5105 Evaluate side-chains 209 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain F residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN D 72 HIS D 104 ASN G 373 GLN H 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113286 restraints weight = 56211.542| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.39 r_work: 0.3060 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15415 Z= 0.160 Angle : 0.557 11.225 20966 Z= 0.305 Chirality : 0.066 1.418 2513 Planarity : 0.005 0.059 2728 Dihedral : 4.610 18.123 2161 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.92 % Allowed : 8.69 % Favored : 90.39 % 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 aren not related in a simple way. whole: 1.33 (0.18), residues: 1974 helix: 2.06 (0.18), residues: 746 sheet: 1.14 (0.25), residues: 381 loop : -0.29 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 179 TYR 0.014 0.002 TYR G 34 PHE 0.017 0.002 PHE E 198 TRP 0.010 0.002 TRP A 30 HIS 0.009 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00332 (15415) covalent geometry : angle 0.55663 (20966) hydrogen bonds : bond 0.05298 ( 860) hydrogen bonds : angle 5.32480 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14886.66 seconds wall clock time: 251 minutes 42.80 seconds (15102.80 seconds total)